The thirteenth Karmapa, Dudul Dorje (1733-1797), was born at Champa Drongsar in South Tibet, and once located by Situpa, brought to Tsurphu at the age of five. In a further escalation of the sectarian politics of the time, the then ruler of Tibet, the seventh Dalai Lama, Kalzang Gyatso, with his prime minister, Sonam Topgyal, instituted a rule that all government officials must be Gelugpa.

As a consequence of this, the Dalai Lama's approval of the new Karmapa incarnation was required. Finally, though, the thirteenth Karmapa and the ninth Shamarpa, Geway Jungnay, were enthroned. The Karmapa received full teachings from Situpa, but the Shamarpa only lived for eight years, precipitating another controversy. Subsequently, Dudul Dorje and Situpa, once again helped by Kato Rigdzin Tsewang Norbu, recognised Shamarpa's reincarnation in a younger brother of the fourth Panchen Lama, Palden Yeshe.

The seventh Gyaltsap Rinpoche (1699-1765), however, had already installed a son of the wealthy Ger Namsayling family as reincarnation, with the approval of Shamarpa's monks at Yangpachen monastery, his principal seat in Tibet. The dispute eventually reached the courts, where it was decided that the Karmapa had indeed located the true incarnation.