The Shogun Monastery was the first monastery of the Martsang Kagyu tradition and was constructed in 1167, in Dang-Di in Markham, Tibet, by Choje Marpa Sherab Yishi, the founder of the lineage.

Choje Marpa studied at the famous Sangpu Institute, under the Kadampa tradition, before becoming one of the eight heart disciples of Phagmodrupa, a heart disciple of Gampopa, the founder of the Kagyu School of Tibetan Buddhism. Choje Marpa established the Martsang Kagyu tradition as a union of the Kadampa and Kagyu lineages, combining the teachings of the sutra and Vajrayana with his own practical experiences.

Choje Marpa established the Shogun Monastery to pass on his teachings. The Monastery had a unique system, where students had to apply for teachings, and undertake various tests, before they were permitted to stay on retreat and practice in the mountains of the monastery. Once accepted, students received direct teachings in the oral lineage and gained esoteric knowledge of Buddhism. This stringent and unique teaching method outlived many qualified practitioners, who after their retreat and practice achieved the realization of rainbow body. Martsang Kagyu then became famous in Tibet and the number of applicants rapidly increased.

Drogon Rinchen was one of the most trustworthy and dedicated disciples of Choje Marpa, who received the true essence of the teachings and was an exceptional practitioner and scholar. Whenever Choje Marpa went on retreat, Drogon Rinchen took responsibility for all of the Shogun Monastery affairs and teaching.

However after Choje Marpa passed away, Drogon Rinchen transferred the abbot position at the Shogun Monastery to his senior fellow classmate, YiShi Gyaltsen (1185-1245), who was the first Khenpo at the Shogun Monastery. While YiShi Gyaltsen served as the abbot, the number of monks in the Monastery increased to over two thousand and the monastery became the largest in Tibet at that time.