The first incarnation of Most Venerable Bongtrul Rinpoche's line was Lho Tsele Lhundrüp. He was named after his birthplace – Lho. There are three other associated incarnations who share the name Lho:  Lho Chen Rinpoche, Lho Kunsang Rinpoche, and Lho Bongtrul Rinpoche.  The second incarnation was Lho Drupchen Tenzin Sangpo. The third incarnation was Lho Tenzin Jangchub Sangpo. The fourth incarnation was Lho Jedrung Orgyen Nüden Dorje Rinpoche.

Lho Jedrung Orgyen Nüden Dorje was the holder of seven transmission lines and an accomplished master of both the Kagyu and Nyingma traditions. His line begins with Shri Simha and proceeds through Nyatri Tsepo (the first Tibetan Dharma King) and Nyang Tenzin Sangpo (a disciple of Padmasambhava ). Lho Jedrung Orgyen Nüden Dorje also manifested as Namkha Wangchuk (in the family lineage of Drugyal Kyura Dong); Dungtso Repa (the Tertön who revealed the Dzogchen Yangti Nagpo); Ngakchang Yeshe Dorje (Jnana Benza, son of Tertön Sangye Lingpa); Orgyen Ledro Lingpa; and finally as an incarnation in the gö kar chang lo family line of Shotang (descending from Ratna Lingpa - an unbroken family line of accomplished naljorpas and ngakpas).

The fifth incarnation was Lho Jedrung Tenzin Gyalbu Nyugü Rinpoche. The sixth incarnation was Lho Bongtrul Tenzin Drodul Rinpoche (the sixth Lho Bongtrul was the Tsawa'i Lama of both the Drigung Kyabgons, the fifth Chuntsang Chökyi Lodrö, and the fifth Chetsang Thugje Nyima). The seventh incarnation Most Venerable Lho Bongtrul Tenzin Nyima is also the Mind incarnation of the first Lho Tsele Lhundrup. He has two brothers who are his close disciples. The elder brother is Ongchen Kunsang Drodul (Ongtrul Rinpoche, a ngak'phang Lama who is the emanation of Khyechung Lotsa).  The younger brother is Chungpo Drubgyu Tenzin Rinpoche.

The seventh incarnation – Most Venerable Bongtrul Tenzin Nyima Rinpoche – was born in the year 1965. As a boy he attended an ordinary local school and learned how to read and write. As a natural gö kar chang lo master, he taught himself drawing, Tibetan brush calligraphy, and thangka painting.

When he was eighteen years old, Bongtrul Rinpoche entered Lho Lungkar Gompa where he received teachings on Dzogchen and especially Dzogchen Togal from Togden Drogön Rinpoche, a direct disciple of the former Bongtrul Rinpoche. From this Master he also received teachings on the Gongpa Yangzab (dgongs pa yang zab – a Terma revealed by Rinchen Phuntsog, 1509-1557) and Phowa. According to the prophecy of Achi Chökyi Drolma, Togden Drogön recognised Bongtrul Rinpoche as the Mind emanation of Lho Bongtrul and made it known.

At this time Most Venerable Bongtrul Rinpoche had already mastered the chants, rites, and rituals of Lho Lungkar Gompa. Later, he received teachings on the Ground, Path and Fruition from Drubwang Pachung Rinpoche. He received the Drigung Kagyüd Lineage of the Six Yogas of Naropa and the Five-fold Path of Mahamudra from meditation master Tenzin Nyima, a disciple of Drüpwang Achung Rinpoche. He received ordination from Sogtrül Rinpoche of Drigung Til, who gave him the name Könchog Tenzin Thrin-le Tha-ye. Most Venerable Chetsang Rinpoche subsequently recognised him as the Mind incarnation of Lho Bongtrul Rinpoche and gave him the name Könchog Tenzin Sherab Jungne Pal-sangpo.

Most Venerable Bongtrul Rinpoche completed a four-year retreat and other lengthy retreats on Dorje Shinje and Dzogchen Yangzab Terma practices from Dzogchen Khenpo Thubten Namgyal. He received empowerments of the Uttara Tantra, and the Kagye Drubthab of the eight herukas, Dorje Phurba, and Rigzin Jigme Lingpa's Dzogchen teachings. In 1997 Bongtrul met His Holiness Drikung Chetsang Rinpoche. He then received teachings and empowerment on the Five Treasuries of Jamgön Kongtrul Rinpoche containing the quintessential Kagyu empowerments from Garchen Rinpoche, Dölmo Chöje Rinpoche, and Gyalpo Rinpoche.

Bongtrul Rinpoche then went to Drigung Til and sought the guidance of the meditation master Tenzin Nyima Rinpoche on the Six Yogas of Naropa and the Five-fold Mahamudra teachings. His Eminence introduced the yearly practice of the Kagye (the Eight Heruka Drubthabs), the Assembly of Rigzins, the Embodiment of Intentionality of the nature of Mind, Dorje Phurba, and the Lho Lungkar Gon tradition of the Mind Propitiation of the Dechen Nyingpo (bde chen snying po - Essence of Great Bliss).

Most Venerable Bongtrul Rinpoche introduced the entire range of Vajra Dances to Lho Lungkar Gompa. Seeing the needs of future generations, he composed many drubthabs (methods of accomplishment – sadhanas) and Songs of Realization. His Eminence also recorded two audio cassettes of Dharma songs. In 1998 Most Venerable Bongtrul Rinpoche rebuilt the historically important Lungkar Bumo Che Chörten. He later re-built Lho Lungkar Gon Monastery and added retreat centres to the complex. In addition he built a medical dispensary for the local people and founded a school for local children.