The Dzongdrakha Lhakhang is located above the two villages of Bondey and Gyepjag which fall under the Luni geog in Paro. It is situated on a cliff known as Dzongdrakha. One can reach the Lhakhang from Bondey in about thirty minutes.

The history of the Lhakhang can be traced back to the visit of Guru Padmasambhava to Dzongdrakha in the 8th century AD. He flew to the sacred site from Drak Karpo in Paro just above Shaba and one can still see the foot prints of Guru Padmasambhava at the base of the cliff.

In the later part of the 13th century a Tibetan saint that belonged to the Neyningpa School, named Lama Kashi Rinchen Samten Pelzang told the Dubthob (siddha) Jawai Aenpo Gonpo Dorji of the Jangdra Tagtse Monastery in Tibet about the sacred Nye (holy site) of Dzongdrakha at Paro. After receiving this information in around 1429 Dubthob (siddha) Gonpo Dorji began his journey towards Bhutan in search of the sacred Nye. On reaching the village of Jiva on the right banks of river Pachu in Paro, he became lost; all sense of direction had abandoned him. While unsure of his next move he came across a female wolf who guided him towards Dzongdrakha. From this incident the place where the Lam met the wolf came to be known as Wachu which is today known as Woochu, a corrupted form of the former. Further on before reaching Dzongdrakha, the Lam met a dumb boy. The dumb boy on seeing the Lam is supposed to have cried out, “Mother a guest is approaching and its’ going to start to rain too.” The mother out of sheer happiness broke out into uncontrollable laughter that her dumb son could speak and the place came to be known thereafter as Gadrak Wang or place of excessive laughter. However it is known today as Gyepjag Nang. The Lama built the Changchu temple next to the house of the dumb boy. The original structure was washed away due to a flood in 1968 and a new one was built at the site by the people.

Finally before reaching Dzongdrakha, the Lama reached a small plain where he came across a female goat (nanny). The goat was the mount of the deity Nedag Dorji Lekpa that was sent to receive him. On seeing the Lama approaching the goat let out drops of milk that fell onto a large stone slab. Using the milk as ink the Lama scribbled the six syllable mantra of Chenrizig (the Bodhisattava of compassion) Om Ma Ni Padme Hung. Later the stone was placed inside a chorten as the main relic and the chorten came to be known as ‘Om Ma Ni Chorten’ that can be seen even today. The Lama later realised that the goat was no other than the riding horse of the deity of Dzongdrakha Damchen Dorji Lekpa and taking it as an auspicious sign proceeded towards the sacred cliff.

On reaching Dzongdrakha the Lama Dupthob Gonpo Dorji began his meditation. During one of these sessions he was visited by Guru Padma Sambhava who presented him with a crystal sword. The sword became fixed to a rock that resembled a male donkey and a frog. The rock with the sword stuck on it rolled towards him. Inside the rock the Lam came across a crystal Chorten measuring the length of an arrow, a Ringsel (body relic) of Buddha Kasyapa and three Garuda eggs. Two eggs seemed to have flown off. Taking with him the crystal chorten, the Ringsel and the remaining egg the Lama travelled to Bondey and sought shelter in a farmer’s house.

Later he went back to Dzongdrakha and on a cliff that resembled a lion built a chorten. Inside the chorten he placed the crystal chorten, the Ringsel and the egg. This chorten is known as the Shel (Crystal) chorten. The chorten was later consecrated by Dubthob Thangtong Gyalpo on a visit to Dzongdrakha.

The Lama did not have any children but from his reincarnation the lineage of the Dzongdra Chojie was founded. In the 14th century his reincarnation, Lam Neten Jangchub Zangpo built a temple dedicated to the Guru. On the right side of the chorten is the temple of the three Buddhas built by the reincarnation Lama Phan Thog. To the left of the chorten is the temple of the female Goddess Tashi Tsheringma (Goddess of Long Life). Next to the temple of Tashi Tsheringma is the temple dedicated to Sangay Mithrukpa (Akshobya). This was built by Lam Rabten and Lam Phan Thog.

In the Guru Lhakhang there is a statue of two khandroms (dakinis) and the statue of the eight manifestations of Guru Rinpoche. In the Tsheringma Lhakhang there are the statues of Tsheringma and Lord Buddha.

The highlight of the Dzongdrakha is the annual Tshechu (festivals of mask dances) performed from the 8th to the 10th days of the 2nd month. They also have a day long festival on the 16th day of the 2nd month. It is believed that since the masked dance of the 16th day is performed after the last day of the masked dance in the Paro Dzong people must witness the masked dance on the 16th day to properly complete the ceremony.