According to Chhojugun Lhosar Ngagyen, in the 13th century, a Ngingmapa lama, Karzhi Rinchen Samten Pelzang dreamt of a khandrum, instructing him to go to a place called Zhungphug in Moen Yuel, where the treasures of Ugyen Rinpoche were hidden. Lam Karzhi Rinchen Samten Pelzang then shared his dream with a dedicated disciple, Drupthog Gyenpo Dorji from Latoet Jangdrog Taktsheit who later followed the instruction given to Lam Krzhi Rinchen Samten Pelzang by the khandrum in his dream.
A day came, while meditating, when he had a spiritual vision of Guru Rinpoche giving him a crystal sword, with which he hit the cave and a huge rock fell in front of him. It is believed that from this rock, he found a crystal stupa (chorten) which was as long as an arrow and three egg-shaped relics of Sangay Youelsum (karshapa). Two of the three relics are said to have flown away at that very instant. Drubthog Gyonpo Dorji then took the remaining one relic and the stupa in a sack and reached a valley. The people in this valley, having known about the treasure inside the sack claimed it to be theirs. They said that it belonged to them and also said that it was only them, who had the rights over the treasure. Because of this, this valley came to be known as “Bangdey” which is known as “Bondue” today.
The Drubthog later constructed a Lhakhang and installed this treasure (the crystal stupa and the relic) as a sacred monument inside it and named it as Dzongdrakha Goemba. Damchhoen Dorji Legpa was the deity of the Lhakhang, who protected the Lhakhang and the sacred monument inside it. It is believed that the relic used to shake on the auspicious days, because of which the people named the crystal stupa Chorten Karmogyel. The Drubthog, who had spent all his life in this Lhakhang ultimately died there. After the death of Drubthog Gyonpo Dorji, his reincarnations started the lineage of Dzongdra Chhoeje and also built many Lhakhangs and Monasteries in and around the place. It is also said that sometimes later the Rinpung Neten (the head lama of a Dratshang) Jangchung Zangpo, renovated the Lhakhang and built a new chorten in front of the Lhakhang.