The Panchen Lama line of incarnation (tulku) was started by the Fifth Dalai Lama in 1667. Regarded as emanations of Amitabha Buddha their principal seat of power is the Tashi Lhunpo monastery at Shigatse in Tsang Province.
The monastery of Tashi Lhunpo was founded by Gendun Drub, who was later to be posthumously acknowledged as the 1st Dalai Lama. It was the tradition of the monastery that each successive abbot have the title of Panchen. After the time of Lobzang Chokyi Gyaltsen, the 5th abbot, the title of Panchen became the official name of his successive reincarnation lineage. Three previous abbots of Tashi Lhunpo were also posthumously named Panchen incarnations.
There are two systems commonly employed for numbering the Panchen Lamas. The first and earliest system used by the Ganden Podrang and Lhasa administration begins with Panchen Chokyi Gyaltsen (1570-1662), teacher of the 5th Dalai Lama as the 1st Panchen Lama. The second system which arose later likely in the late 18th and 19th centuries with the Panchen Labrang of Tashi Lhunpo begins with Kedrub Geleg Pal Zangpo (1385-1438) as the 1st Panchen Lama. Kedrub was a direct student of Tsongkapa. The followers of the Panchen Lama, Tashi Lhunpo Monastery and the Chinese Governmennt follow the Panchen Labrang manner of counting. The Ganden Podrang and many if not all Western scholars have used the earlier system beginning with Chokyi Gyaltsen as the 1st Panchen. It is now common to find in publications and literature both numbers side by side to remove any confusion as to the correct Panchen that might be referenced. There is certainly a degree of politics as to how and why the two competing systems have developed and who adheres to which system.
There are also several lists naming the various pre-incarnations of the Panchen Lama. The longer lists include Padmasambhava and Jowo Atisha. In the  first and shortest list only four Indian teachers are included: Subhuti, Yashas, Bhavaviveka and Abhayakara Gupta. In the  second list Padmasambhava and Atisha are added for a total of six Indian pre-incarnations. In the third and longest list a further four Indian teachers are included. At least two of those are mahasiddhas with one identified as Ghantapa.
Jeff Watt 4-2003
Biography: Lobzang Chokyi Gyeltsen (blo bzang chos kyi rgyal mtshan) was born in a village called Drukgya (brug brgya) in the Lhan valley, in Tsang, in either 1567 or 1570. His father, Kunga Ozer (kun dga' 'od zer), was a nephew of Wensa Sanggye Yeshe (dben sa sangs rgyas ye shes, 1525-1590/1591), and a member of the illustrious Ba (sba) clan. His mother's name was Tsogyel (mtsho rgyal). They gave him the name Chogyel Pelden Zangpo (chos rgyal dpal ldan bzang po). The boy was recognized by Langmika Chokyi Gyeltsen (glang mig pa chos kyi rgyal mtshan) as the reincarnation of Wensapa Lobzang Dondrub (dben sa pa blo bzang don sgrub, 1505-1566) and given the name Chokyi Gyeltsen.
As a youth Chokyi Gyeltsen studied with Sanggye Yeshe, then the abbot of Tashilhunpo (bkra shis lhun po) and Wensapa monasteries (dben sa pa). For the first years of his life he was tutored in the autumn by Sanggye Yeshe in Drukgya, receiving from him many blessings and empowerments. There he also received teachings and initiations from his brother and grandfather. At the age of thirteen Chokyi Gyeltsen left Drukgya for Wensa monastery, to further his instruction with Sanggye Yeshe. He took novice vows with his master, and received the name Lobzang Chokyi Gyeltsen, and began instruction in Lamrim (lam rim). Chokyi Gyeltsen remained at Wensa for the next five years.
In his eighteenth year Chokyi Gyeltsen went to Tashilhunpo where he entered the Tosam Ling college (thos bsam gling grwa tshang), studying with Peljor Gyatso (dpal 'byor rgya mtsho, d.u.). He spent the next three summers at Wensa, however, receiving further teachings and transmissions from Sanggye Yeshe, including the Ganden Mahamudra of Tsongkhapa. In 1591 he received the news that Sanggye Yeshe was ill with smallpox, and he quickly returned to visit with him one last time, shortly before Sanggye Yeshe passed away. Following a successful examination in Pramanavarttika at Tashilhunpo, Chokyi Gyeltsen returned to Wensa to oversee the funeral.
Chokyi Gyeltsen ordained that same year, 1591, with Panchen Damcho Yarwel (paN chen dam chos yar 'phel, d.u.), Peljor Gyatso, and Pa?chen Lhawang Lodro (paN chen lha dbang blo gros, d.u.) officiating. He then traveled to Lhasa, making offerings at the Jokang and proceeded to Ganden, where he continued his education with Namkai Tsenchen (nam mkha'i mtshan can, d.u.), with whom he studied Kalacakra, and Gendun Gyeltsen (dge' 'dun rgyal mtshan, 1532-1605/1607), the Twenty-eighth throne holder of Ganden, who taught him the collected works of the Second Dalai Lama. Chokyi Gyeltsen in turn taught Gendun Gyeltsen the Ganden Mahamudra, making him his successor in the oral lineage of that tradition. Damcho Pelbar (dam chos dpal 'bar, 1523/1546-1599), the Twenty-sixth throne holder of Ganden, also taught him Cho.
Having returned to Wensa, which he enlarged with new temples and statues, Chokyi Gyeltsen gave public teachings on Lamrim and other topics, but soon felt the urge to enter retreat. He closed himself off from the public for six or seven months, reading scripture between sessions of meditation. It was during this short retreat that he had a vision of Tsongkhapa, and in his sleep received a number of important transmissions from him. He shifted his retreat to his home village, living for a time like a “cotton-clad one” (ras pa) in the tradition of the Kagyu ascetics, before returning to Wensa.
In 1601, his fame now widespread, Lobzang Chokyi Gyeltsen was asked to assume the abbacy of Tashilhunpo. The thirty-one year old was already abbot of Wensa and, beginning in 1598, abbot of Gangchen Chopel (gangs can chos 'phel), having been requested to assume that post by Lhuntse Depa (lhun rtse sde pa, d.u.). That same year he initiated a Great Prayer Festival, or Monlam Chenmo (smon lam chen mo) at Tashilhunpo, installing a number of new statues in the temples. Eight years later, in 1609, he established a tantric college at the monastery, the Tashilhunpo Gyupa Dratsang (bkra shis lhun po rgyud pa grwa tshang)
Soon after taking the abbacy of Tashilhunpo, Yonten Gyatso (yon tan rgya mtsho, 1589-1616), the Fourth Dalai Lama, visited there, arriving in Tibet from Mongolia for the first time. It would seem that Chokyi Gyeltsen played a role in the Tibetan acceptance of the Mongolian boy as the legitimate incarnation of Sonan Gyatso (bsod nams rgya mtsho, 1543-1588). The Fourth Dalai Lama requested Chokyi Gyeltsen accompany him to Drepung, where he taught for some time, and then as he traveled to various Kadampa and Gelukpa monasteries in the region, including Reting (rwa sgreng) and various sites connected to Tsongkhapa's activities in Lhoka.
In 1612 Chokyi Gyeltsen visited Bhutan on invitation from the Lhapa hierarchs of Nyo (gnyos). This clan, Drukpa Kagyu followers who were strong in both Tsang and Bhutan, were rivals to Zhabdrung Ngawang Namgyel (zhabs drung ngag dbang rnam rgyal, 1594-1651). Their loss of influence in Bhutan, and the close relations with Chokyi Gyeltsen, led to the Lhapa conversion to the Geluk tradition late in the century. They were but one clan-based religious tradition that Chokyi Gyeltsen brought under the Geluk tradition. Chokyi Gyaltso was again involved in Bhutanese-Tibetan affairs, negotiating a truce to conflicts between the two in the mid-1650s. Among hostages freed by Bhutan was a son of the house of Nenying (gnas rnying), another clan-based religious tradition whose merger with the Geluk was accomplished by Chokyi Gyeltsen.
Chokyi Gyeltsen continued to go back and forth between Zhigatse and Lhasa, teaching at Tashilhunpo, Drepung, Sera, Ganden, and other Geluk monasteries. In 1617 the Fourth Dalai Lama passed away, and Chokyi Gyeltsen assumed the abbacy of both Drepung and Sera. These were not the last monasteries where he served as abbot; in 1626 he was made abbot of Ganden's Jangtse college, and in 1642 of Zhalu (zha lu).
In 1618 the ruling family of most of Tibet, the Pakmodrupa (phag mo dru pa), was overthrown by the ruling family of Tsang, based in Zhigatse. Supporters of the Kagyu tradition, the new rulers repressed Gelukpa institutions and religious practice, including the large Geluk monasteries of the Lhasa region, although he tolerated the presence of Tashilhunpo and Chokyi Gyeltsen. Curing him of a disease the King believed to have been inflicted by the Fourth Dalai Lama, Chokyi Gyeltsen was able to secure permission from the King of Tsang to confirm the reincarnation of the Fourth Dalai Lama in the person of a boy he named Lobzang Gyatso (blo bzang rgya mtsho, d.u.), although he was forbidden to install him in Lhasa.
Over the next decade relations between Lhasa and Zhigatse continued to deteriorate, and Chokyi Gyeltsen was forced to mediate time and again. He was also forced to confront Mongol invasions, first in 1621 when Mongolian troops, brought in after secret negotiations with Geluk heirarchs, laid seige to Tsang authority in Lhasa and drove Tsang forces to Chakpori (lcags po ri), a small rocky hill in Lhasa. Only after Chokyi Gyeltsen's intervention were the forces allowed to retreat to Zhigatse. With Tsang forces out of Lhasa, in 1622 Chokyi Gyeltsen was able to enthrone the Fifth Dalai Lama at Drepung.
Following the defeat of the Tsang King and the ascent of the Fifth Dalai Lama as King of Tibet in 1641, the fortunes of Chokyi Gyeltsen grew greater still. Chokyi Gyeltsen was given the title of Pa?chen Lama. Two separate systems of enumeration exist; according to the system of Tashilhunpo, three previous lamas, identified as Chokyi Gyeltsen's previous incarnations, are identified as the First through Third Pa?chen Lamas: Khedrubje Gelek Pelzang (mkhas grub rje dge legs dpal bzang, 1385-1438), Sonam Chokyi Langpo (bsod nams phyogs kyi glang po, 1439-1505), and Wensapa Lobzang Dondrub. For this reason Chokyi Gyeltsen is either listed as the First or the Fourth Pa?chen Lama (the convention used on the Treasury of Lives is to list him as the Fourth, following common standard).
Chokyi Gyeltsen continued to teach for the next two decades, passing away in 1662.Bibliography:
Blo bzang chos kyi rgyal mtshan. 1973 (1720). Chos smra ba'i dge slong blo bzang chos kyi rgyal mtshan spyod tshul gsal bar ston pa nor bu'i phreng ba. In Collected Works (Gsung 'bum) of Blo bzang chos kyi rgyal mtshan, the 1st Pa?chen Lama, reproduced from tracings from prints of the Bkra shis lhun po blocks, pp. 5-454. New Delhi: Mongolian Lama Gurudeva. Also published as The Autobiography of the First Pa?chen Lama Blo bzang chos kyi rgyal mtshan, 1969, Delhi: Ngawang Gelek Demo.
Kapstein, Matthew. 2006. The Tibetans. Boston: Blackwell Publishing, pp. 134-139.
Smith, Gene. 2001. “The Autobiography of the First Pa?chen Lama.” In Among Tibetan Texts, pp. 119-131. Boston: Wisdom Publications.
Tshe mchog gling yongs 'dzin ye shes rgyal mtshan. 1970 (1787). Biographies of Eminent Gurus in the Transmission Lineages of the teachings of the Graduated Path, being the text of: Byang chub Lam gyi Rim pa'i Bla ma Brgyud pa'i Rnam par Thar pa Rgyal mtshan Mdzes pa'i Rgyan Mchog Phul byung Nor bu'i Phreng ba. New Delhi: Ngawang Gelek Demo, vol 1, pp. 88-235.
Willis, Janice D. 1985. “Preliminary Remarks on the Nature of rNam-thar: Early dGe-lugs-pa Siddha Biographies.” In Soundings in Tibetan Civilizations. Barbara Aziz and Matthew Kapstein, eds. Delhi: Manohar, pp. 304-319.
Willis, Janice D. 1995. Enlightened Beings: Life Stories from the Ganden Oral Tradition. Boston: Wisdom Publications, pp. 85-96.