Crows and the “Men in Black” are recurring themes in many Tibetan Buddhist stories, especially in legends of Mahakala and the histories of the Dalai Lama. Both Mahakala and the Dalai Lama are emanations of Avalokiteshvara / Chenrezig.
“You come from your tree…
You, the Great Black One, the Great Crow.
Glorious Six-Armed One, homage and praise to you!
Sternly protect the doctrine of the Buddha!” 
“Mahākāla is the most commonly invoked of all Dharma protectors, and is important to all schools of Tibetan Buddhism. In Tibetan he is often known simply as ‘the Lord’,” writes Vessantara. 
Mahakala, crows and the Dalai Lama
Black six-armed Mahakala is a manifestation of Chenrezig, the Buddha of Compassion, and among the most important of deities in Vajrayana Buddhism. The Dalai Lama is also an emanation of Avalokiteshvara (Chenrezig). In an interview, the Dalai Lama told the story of the two crows in his own life (on his official website):
“Another thing I didn’t mention in my autobiography is that after my birth, a pair of crows came to roost on the roof of our house. They would arrive each morning, stay for while and then leave. This is of particular interest as similar incidents occurred at the birth of the First, Seventh, Eighth and Twelfth Dalai Lamas. After their births, a pair of crows came and remained. In my own case, in the beginning, nobody paid attention to this. Recently, however, perhaps three years ago, I was talking with my mother, and she recalled it. She had noticed them come in the morning; depart after a time, and then the next morning, come again.
“Now, the evening after the birth of the First Dalai Lama, bandits broke into the family’s house. The parents ran away and left the child. The next day when they returned and wondered what had happened to their son, they found the baby in a corner of the house. A crow stood before him, protecting him.
“Later on, when the First Dalai Lama grew up and developed in his spiritual practice, he made direct contact during meditation with the protective deity, Mahakala.
At this time, Mahakala said to him, Somebody like you who is upholding the Buddhist teaching needs a protector like me. Right on the day of your birth, I helped you.
“So we can see, there is definitely a connection between Mahakala, the crows, and the Dalai Lamas.” 
Dhe-Tsang Monastery: crows and men in black
In the beautiful story of the founding of Dhe-Tsang monastery, the great protector Black Mahakala personally guided Je Tsongkhapa’s great disciple Ngawang Drakpa — appearing as a black crow.
The monastery, built in the year 1414, owed its existence to the coming of a great black crow. Later, another crow carried a powerful sadhana from Lama Tsongkhapa to his disciple to help subdue the demons and black magic troubling the area. Then, came the “Men in Black” who mysteriously appeared, and who later transformed into three statues — one of Six-Armed Mahakala, one of Four-Armed Mahakala, and one of White Mahakala.
We can see these stories as symbolic, literal or magical, but they immediately give us a sense of power and importance of Mahakala. Whether as a potent psychological archetype or as an Enlightened Deity active in the world, Mahakala — the fierce aspect of Chenrezig or Avalokiteshvara, Buddha of Compassion — the symbolism of the history is profound. Whether Mahakala’s activity is all in “your head”, or actually active in the relative world (Desire Realm), there can be no doubt (to a Vajrayana Buddhist) that Black Mahakala’s power is irresistible. Even today, in some monasteries, the monks put aside a portion of food for “the black man” Mahakala. In Mahakala Tangkhas, you often see the black man in the foreground.
There can be no doubt that all of these manifestations in the stories — the crows and the three men in black (or three black men, depending on the translation) — are none other than emanations of The Great Black One, Mahakala.
First, comes the Crow
In the wondrous tale of Dhe Tsang Monastery, Mahakala manifests as both crows and the three men in black (or black men, depending on the translation). From a wonderful article by Nitin Kumar :
“The Dhe-Tsang monastery, built in 1414 by a close disciple of Je Tsongkhapa is situated in the Gyalrong district of eastern Tibet. When its founder, Ngawang Drakpa, came to the region intending to build a monastery there, he realized that the place was special but couldn’t decide on the best location to build the Hermitage.
At that very moment, a huge crow swooped down on him, picked off his scarf, and flew away with it. The monk hastened to follow the crow. Eventually, the garment was found hanging from the branches of a Juniper tree. Here it is relevant to observe that the crow is visualized in Tibetan Buddhism as an incarnation of Mahakala, whose name literally means the ‘Great Black One.’
Taking this occurrence to be an auspicious omen, Ngawang decided to build the monastery around the tree, which would itself serve as a natural pillar of the prayer hall.”
This was only the beginning of this tale of wonders. Later, when demons and black magic caused the monastery construction to collapse — whatever was built each day, would crumble that night — Ngawang Drakpa again relied on the great Lama Tsongkhapa’s advice — and the crow emanation of Black Mahakala.
As he was considering what to do, the crow appeared again. “Much relieved by its presence, the venerable monk wrote a letter to his guru Tsongkhapa in Lhasa, asking for help. The master in response to his pupil’s plea then composed a practice brimming with spiritual potency and gave it the name: ‘The Solitary Hero Vajra Bhairava Sadhana.’ He gave it to the crow to deliver it to Ngawang Drakpa. When the latter received the manual, he performed the practice immediately…” All negative influences were subdued. 
Then, the Men in Black (or the Black Men)
From then on, construction went smoothly. Venerable Ngawang Drakpa sought out the best possible sculptors to create the statues for the monastery, and especially the great protector Mahakala. Again, quoting the feature by Nitin Kumar:
“When the major part of construction was completed, the lama began to look for master sculptors who could create spiritually charged images for the retreat. One day, three black men came to the monastery and stayed there for some time. They later revealed that they were sculptors from India. Delighted on hearing this, Ngawang Drakpa eagerly sought their services in building the required deity statues. Of the three men from India, only one agreed to stay on and help. As per his promise, the sculptor created all the statues requested except that of Mahakala, which alas, was only half-finished when the day of inauguration arrived.
The celebrations for the occasion consisted of various ritual dance performances. At the end of the program, the Indian sculptor declared that he too wished to perform a dance for the contemplation of the audience and proceeded to enthrall them with an exceptionally energetic performance wearing a swirling costume and a large wrathful mask, leaving the viewers in raptures. Towards the conclusion of the dance, his physical form suddenly started to shrink until finally only the giant mask remained on the ground and there was no trace of the body of the dancer. Taken aback by the bizarre turn of events, the monks rushed to the chamber where the half-finished statue of Mahakala lay. To their utter surprise, the statue was complete. The sculptor had merged with his creation, granting it an unparalleled spiritual potency.
The story does not end here, however. Later they were informed that the two companions of the Indian sculptor, who had declined to stay on, had each made a Mahakala statue at two different monasteries and had likewise mysteriously disappeared into their respective creations. It was not long before the perceptive adepts realized that these sculptors were none other than the great god Mahakala in his various manifestations, incarnating himself as the savior and protector of monasteries. Thus at Ngawang’s hermitage he was the Six-Armed Mahakala and had created a sculpture of himself with half-a-dozen hands. In a similar manner the other two had created icons of the Four-Armed and the White Mahakala respectively. Collectively, they were named the three Mahakala brothers and became vastly popular all over Tibet.”
Crow in different traditions
In Tibet — and most cultural traditions not influenced by the story of Noah (where the crow failed his mission — the crow is considered highly auspicious. In Tibet crow is associated with Mahakala; in Europe with Odin; in North American native spirituality, Raven is an important entity and Crow is sometimes the totem of the Great Spirit; in Hinduism, crow is associated with Shiva.
The crow and the Dalai Lamas
The crow also features in both the stories of the first — and the current — Dalai Lamas.
“When the home of the baby who was to become known as the First Dalai Lama Gedun Drupa Chokey Geundun (or, Kundun which means “the presence” ) was set upon by raiders, the family had to flee leaving behind the little child. When they returned the following morning, they found the baby guarded by a pair of crows. To this day, crows figure among the symbols of his rank.
In Kundun (Martin Scorsese, 1997) the film made of the first 25 years of the current (14th) Dalai Lama’s life based upon a series of interviews conducted by Martha Mathison, Reting the Regent tells how on the morning following the birth, the mother noticed a pair of crows outside.” — Raven and Crow Khandro.net
Why Mahakala appears as a wrathful deity
Ven. Khenpo Karthar Rinpoche explains:
“It is not because there is something ferocious about Mahakala or that he is aggressive. Mahakala is none other than the inseparability of compassion and loving-kindness. In the view of ultimate wisdom, there is no separation between the Awakened Mind of Buddha and that of Mahakala. Mahakala is a manifestation of the awakened mind.
Appearing in very majestic form, splendid yet frightening, Mahakala stands in the midst of a mountain of flames to symbolize that no enemy can stand this appearance aspect; the sharp chopper, which he holds aloft in one hand, symbolizes the cutting through of negative patterns, aggression, hatred, ignorance–any of the five poisons. No neurosis or negativity can tolerate this very majestic form; the frightening form symbolizes Mahakala as totally devoid of fear or hesitation in his spontaneous yet consistent work toward the benefit and liberation of all beings.
Mahakala is seen standing on the corpse of two human bodies, thus symbolizing the death of negativities and the complete uprooting of negative patterns to such a point that, like a dead body, they will not come to life. It is very important that we know these symbols of Mahakala because many times we have mistaken notions that he may be a clinging spirit or harmful, evil being, perhaps even the Lord of Death ready to devour and attack. One would find great difficulty in relating to the various symbols without understanding that our awakened compassion is the essential quality of the being of Mahakala. Mahakala has never been known to harm one being, even in the slightest manner, because he is constantly benefiting beings through the continuous play of the enlightened mind.” 
Vessantara’s story of Chenrezig’s transformation
In his wonderful book “A Guide to the Deities of Tantra” author and teacher Vessantara gives a lovely prose visualization to help explain the transformation of peaceful to wrathful :
“Avalokiteśvara, the Lord of Compassion, gazes out across the world, his white radiance soothing the sufferings of living beings. With one pair of hands he clasps to his heart the wish-fulfilling gem of his vow to eradicate the world’s pain. In his upper left hand he holds the lotus of spiritual receptivity, the desire to leave the mud of saṃsāra and reach up towards the sun of true happiness.
Above his head we sense the oceanic love of Amitābha, his spiritual father. In Avalokiteśvara’s heart the mantra oṃ maṇi padme hūṃ rotates ceaselessly, pouring its light into the six realms of suffering. In his upper right hand we see his crystal mālā turning. With each bead another being’s sufferings are extinguished. We watch the dancing reflections in the crystal beads, follow their steady rhythm as aeons pass.
Still the beads flow through the milk-white fingers. The pace is steady, smooth, ceaseless. And yet … there is still so much agony, pain, and frustration mirrored in those patient eyes. Hearts which hear the call of the mantra and long to respond are chained by dark forces, restrained by fear, bewildered by confusion, so that they do not know whence the sound comes or how to follow it.
The sapphire eyes cloud with a gathering storm of spiritual impatience. They steal a glance at the steady, but too slow, circling of the crystal beads to their right. They look once more, hard, at the plague forces of ignorance, the jailers of hatred, the ransomers of craving who hold so many beings in their clutches.
The crystal beads begin to change shape. They lose their sparkling reflections for a sun-bleached white. They become a death’s head garland, a rosary of skulls. The delicate white hand grows darker, its light changing from white to deep blue, like an eclipse of the sun.
The powerful hand’s first and last fingers stab the air in a menacing gesture. Around it roars a corona of flames. With a world-shaking cry the figure, now blue-black, starts to its feet. The wish-fulfilling jewel transforms into a vajra-chopper and a skull cup dripping with red nectar. The soft lotus transforms into a trident with a death’s head.
From the huge, overpowering blue-black body another arm thrusts out, rattling a skull drum. To the left a further first uncoils a noose. The giant figure pounds forward, wild hair streaming upward, tied round with snakes. The massive body, nearly naked, girt only with a tiger-skin, wears skulls – pretty, staring skulls – as jewels. Snake-enwreathed, fang-mouthed, three eyes glaring bloodshot from an awesome face, he marches onward bellowing challenge…”
[Read on in Vessantara’s amazing book: A Guide to the Deities of the Tantra.]
Symbolism of popular Six-Armed Black Mahakala
Black six-armed Mahakala is a manifestation of Chenrezig, the Buddha of Compassion. Although he appears wrathful, this is a symbolic appearance that conveys his power to overcome negativities, obstacles and provide conducive conditions for practice. In brief, the complex attributes of six-armed Mahakala are symbolic of:
- Midnight blue or black symbolizes changeless Dharmakaya (all colours absorb into black.)
- Three eyes convey that he sees the past, present and future.
- The five-skull crown: transformation of the five poisons of anger, desire, ignorance, jealousy and pride — into the five wisdoms.
- Six arms represent the attainment of the six perfections: generosity, patience, morality, diligence, meditation, and wisdom.
- Rosary of skulls symbolize continuous activity on behalf of all sentient beings.
- Damaru hand drum represents the sound of emptiness
- The skullcup filled with blood symbolizes either/ both the subjugation of the maras (evil), or the transformation to the pristine nectar of wisdom.
- The kartika or curved ritual knife stands for “cutting attachments” and clinging to “ego.”
- The trident staff shows his power over the three kayas.
- The lasso binds those who break their vows.
- He stands on an elephant-headed deity, symbolizing the overcoming of obstacles (elephants represent pride) and also overcoming obtacles subconscious thoughts
- He stands on a sun disc, symbolizing illumination from ignorance.
- The lotus throne represents purity and the Lotus Family (Chenrezig and Amitabha are Lotus Family.)
- The tiger skin represents the purification of desire.
- The elephant skin stands for purification of pride.
- Snakes represent the purification of anger.
Praise to Black Mahakala
(Normally for a Tea Offering)
NYUR-DZÄ CHÄN-RÄ-ZIk-LA CH’AK TS’ÄL-LO
ZHAP-DUP-D’ANG-CHÄ VINAYAKA NÄN
NAK-PO CH’EN-PO TAK-G’I SHAM-T’AP CHÄN
CH’AK-Dr’UK DrÜL-GY’I GYÄN-GY’I NAM-PAR GYÄN
Quick-acting Avalokita, homage to you!
Wearing anklets, you trample Ganesa.
Mahakala, you wear a tiger-skin loincloth
Fully adorned with snake-ornaments on your six arms.
2. YÄ-PA Dr’I-G’UK B’AR-WA Tr’ENG-WA DZIN
T’A-MA DAMARU-NI Dr’AK-TU Tr’ÖL
YÖN-PA T’Ö-PA D’ANG-NI DUNG TSE-SUM
D’E-ZHIN ZHAk-PA ZUNG-NÄ CH’ING-WAR J’E
The (first) right holds a triku (chopping-knife), the middle a mala,
The last plays violently a damaru;
The left hold a skull-cup, and a three-pronged lance,
And likewise a noose, which serves for tying up.
3. Dr’AK-PÖi ZHÄL-NI CH’E-WA NAM-PAR TSIk
CHÄN-SUM Dr’AK-PO U’TrA GY’EN-D’U BAR
TrÄL-WAR SINDHURA-YI LEk-PAR J’Uk
CHI-WOR MI-KYÖ GYÄL-PÖi GYÄ-TAP TÄN
Your wrathful mouth completely bares its fangs
Your three eyes are fierce. The hair of your head blazes upward.
Your forehead is properly anointed with red lead.
On your crown, Aksobhya’s royal presence is fixed.
4. Tr’AK-DZAK MI-GO NGA-CHÜi DO-SHÄL CHÄN
RIN-CH’EN T’Ö-KAM NGA-YI U-LA GYÄN
SHING-LÄ J’ÖN-NÄ TOR-MA LEN-DZÄ-PÄi
PÄL-DÄN CH’AK-Dr’UK-PA-LA CH’AK-TS’ÄL TÖ
You wear a great necklace of fifty men ‘s heads, dripping blood.
On your crown, you’re adorned with five dry, jeweled skulls.
You come from your tree and accept our torma offering,
Glorious Six-Armed – homage and praise to you!
5. SANG-GYÄ TÄN-PA NYÄN-PO SUNG-WA-D’ANG
KÖN-CH’OK U-P’ANG NYÄN-PO TÖ-PA-D’ANG
DAK-CHAK PÖN-LOP K’OR-D’ANG CHÄ-NAM-KYI
KYEN-NGÄN B’AR-CH’Ä T’AM-CHÄ ZHI-WA-D’ANG
CHI-DÖ NGÖ-Dr’UP NYUR-D’U TSÄL-D’U SÖL!
Sternly protect the Doctrine of the Buddha!
Sternly praise the height of power of the Jewels!
For us – teachers, disciples and entourage –
Please quell all bad conditions and obstructions,
And grant us quickly whatever siddhis we wish!
 One verse from the “Tea offering praise” to Black Mahakala.
 From a teaching given by the Ven. Khenpo Karthar Rinpoche on February 2, 1981 at Karma Triyana Dharmachakra; translated by Ngodrup Burkhar and edited by Agnes M. Ruch.
 “The Many Forms of Mahakala Protector of Buddhist Monesteries” Exotic India by Nitin Kumar
 Questions and Answers with the Dalai Lama.
 Vessantara. A Guide to the Deities of the Tantra (Meeting the Buddhas) . Windhorse Publications. Kindle Edition.
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