Lineage holders are as follows:

H.H. The Jamgon Lama Tsongkhapa-Chenpo
H.E. Jetsun Sherab Sengye

1. H.E. Dhol-Nag-Palden-Sangpo
2. H.E. Rhoktso-Choe-Tse-Nawang Dakpa
3. H.E. Jamyang Gedun Phel
4. H.E. Rabjam-Choeki-Yhing
5. H.E. Lama Tashi Phakpa
6. H.E. Penchen Samdrup Gyalgtso
7. H.E. Nyi-Nying-Choeji Sonam Gyaltsen
8. H.E. Gyuedchen Tsundu Phakpa
9. H.E. Khedrup Dorjee Sangpo
10. H.E. Gyuedchen Sangye Gyatso
11. H.E. Tsechen Jampa Gyatso
12. H.E. Dorjee Chang Kunchok Gyatso
13. H.E. Dejorpa-Khedrup Gendun Gyatso
14. H.E. Lama Rinchen Gyatso
15. H.E. Robjampa-Choekyi-Wangchuk
16. H.E. Phuk-Chenpa
17. H.E. Sherab Rinchen
18. H.E. Palden Chokjin
19. H.E. Choegyal Gonpo
20. H.E. Choklek Woser
21. H.E. Gyued Chen Kunchok Yarphel
22. H.E. Nawang Lobsang Yeshi
23. H.E. Go-mangpo-Rabjam-Mhawa-Loden
24. H.E. Aepa Rabjam-Mhawa-Yeshi
25. H.E. Sed-Gyued Tendar
26. H.E. Sed-Gyued Sangye Woser
27. H.E. Sed-Gyued Dher Hen Nagwang Namgyal

For the period of 1702 to 1932 no records exist. Our knowledge of lineage holders suffers a gap of 230 years. The names of the 28th to the 89th Great Masters are unknown.

90. H.E. Namgyal Chophel
91. H.E. Tsultim Chophel
92. H.E. Palden Gyatso
93. H.E. Markhampa Jampa Tashi
94. H.E. Thubten Dargye
95. H.E. Lobsang Tendar
96. H.E. Trihor Jampa Tashi
97. H.E. Sed-Gyued Dorjee Chang Jampa Wangyal
98. H.E. Gyued-Med Khensur Thutop Gonpo
99. H.E. Gyued-Tod Khensur Ngawang Jorden
100. H.E. Gyued-Med Khensur Lobsang Delek

To the 21st Sed-Gyued Dorjee Chang Kunchok Yarphel, the lineage holders are known as the great Secret whispered Lineage holders. Whispered lineage is secret teaching transmitted only to the closest disciples through direct communication with their root teacher or meditation deity. His Holiness the fifth Dalai Lama too greatly appreciated and declared that Dorjee Chang Kunchok Yarphel as an excellent master and a lord of whispered lineage.

Sed-Gyued Dorjee Chang Kunchok Yarphel once asked Dham-Chen Chogyal, the Great Dharma Protector, to gather before him any suitable disciples as he was quite old. As a result, Jamshed Nawang Tsundu, Cheang-kya Nawang Chokden and other suitable disciples came to Tsang province in Central Tibet to meet Sed-Gyued Dorjee Chang Kunchok Yarphel and received from him empowerments and oral transmissions of Guyasamaja, Heru,-Kapa, Yamantaka and other teachings. Gelukpa Tantras confines within Sed-Gyued Lineage of Traditional Tantras. Besides, Gelukpas Guru Yoga is based on Sed-Gyuedpa's Guru Yoga Gaden Lha-Gyama.

In 2005, due to health problems and old age, H.E. Sed-Gyued Dorjee Chang T.N. Jampa Wangyal Rinpoche requested His Holiness the XIVth Dalai Lama to appoint a Khenpo for smooth running of Sed-Gyued Institute of Buddhist Studies (Monastery), Salugara, India. At present total responsibility to teaching all Sed-Gyued tradition goes to Khenpo who is jointly appointed by H.H. the Dalai Lama and Department of Religion and Culture of the Tibetan Government in Exile. The official tenure of each Khenpo will be three years from the date of assuming responsibility. After completion of three year tenure they will be relieved by H.H. the Dalai Lama and Cultural Department of exile Government by appointing another Khenpo. All the Khenpo so appointed will be the pass-out learned and master philosopher from Gyued-Tod and Gyued-Med Tantric University from South India. The responsibility of Khenpo is particularly to teach Sed-Gyued traditions only. All the responsibility of management of Monastery goes to the elected Governing Body of the Monastery.