They were the basis of the Gelugpa sect in its early stages. Tsongkhapa died in 1419, at which time the sect did not have a system of reincarnation in place to determine the succession of its leader. Tsongkhapa was succeeded in his position as ruling lama, known as Ganden Tripa, by his disciples Gyaltsab Je (the second Ganden Tripa) and Khedrup Je (the third Ganden Tripa and first Panchen Lama). Not long afterward, the newly emerging Gelugpa sect reached a low point when it was attacked by the Rinpungpa family.
At that time, Gedun Druppa (1391- 1474, retrospectively named the first Dalai Lama), a disciple of Tsongkhapa, founded Tashilhunpo Monastery in Shigatse. The monastery became Gelugpa sect’s base in Tsang. When Gedun Druppa died, he was succeeded as Tashilhunpo abbot by a disciple. But some people thought that Gendun Gyatso (1475- 1542, the second Dalai Lama) was the reincarnation of Gedun Druppa and invited Gendun Gyatso to live in Tashilhunpo Monastery. As the Gelugpa sect had no reincarnation system, Gendun Gyatso’s incarnation status could not be established. As the abbot of Tashilhunpo, Yeshe Tsemo, discriminated against him, Gendun Gyatso left Tashilhunpo for Drepung Monastery. He preached in U and enjoyed a good reputation. He founded Chokhorgyal Monastery in Shannan. In 1512, Yeshe Tsemo asked him to return to Tashilhunpo to be its abbot. This demonstrated that, in the Gelugpa sect, the reincarnation system had gained the upper hand over the master-disciple succession. Rinpungpa then prohibited the Gelugpa sect’s monks from taking part iii the Monlam festival held in Lhasa during the first month. However, the Rinpungpa forces were driven out of Lhasa by the Pagtru forces not long afterward. The monks of Drepung Monastery asked to return from Tashilhunpo. In 1517, Gendun Gyatso became the Drepung abbot. In 1518, he presided over the Monlam festival and won back the Gelugpa monks right to take part in it. In 1525, he concurrently took on the post of Sera Monastery abbot. In later generations, each of his successors would concurrently be abbot of both Drepung and Sera monasteries. He enjoyed greater prestige than the Ganden Tripa and became the actual leader of the Gelugpa sect. The Newu Dzongpon granted him a manor, which was renamed Ganden Potrang (Ganden Palace).