The site of Guru Goenpa was founded by Gaylong Lozang Thabkhay who was the 8th reincarnation of Sakteng Kushu Guru in 1851 while he was meditating at Jay Tho Gang in a small goenpa below the present lhakhang. In 1867, the foundation stones of the lhakhang were laid by Lam Kelzang Doyen Tenzin, the 9th reincarnation of Sakteng Kushu Guru. Subsequently, the present lhakhang was constructed by Lam Kelzang Jurmed Namgyel, the 10th reincarnation of Sakteng Kushu Guru, and named it Samten Choeling Goenpa. Until the 11th reincarnation Thubten Kelden, Guru Goenpa was owned and managed privately by the reincarnations and descendants of Sakteng Kushu Guru. 12th Yangsi Tenzin Thinley Namgyel was born on 11th August, 1968 to Yab Lozang Rabten and Yum Tsong Tsong Lopen’s daughter Pema Choden in the place called Ramkem, Arunachal in India. Since the existing reincarnation of Kushu Guru lives in Shar Bumdeling in India, Guru Goenpa Lhakhang had to be managed and taken care of by the Sakteng community.