Khonton Peljor Lhundrub was born in 1561 into the famous Khon clan, an ancient Tibetan family whose members include the founders and present-day throne holders of the Sakya school. His father, Tsewang Norgye, was an important figure in the transmission lineage of the Magical Net Tantra, one of the most important tantric systems of the Nyingma school. Khonton Rinpoche himself came to be considered one of the major figures in the transmission of this tantra. Khontonpa also played an important role in the history of the Gelug school. He was the fifteenth abbot of the Je College of Sera, and he came to be considered one of the lineage masters in the Gelug school's transmission of the "stages of the path" or lamrim teachings. Both the Nyingma and Gelug schools eventually came to consider him a reincarnation of the great Nyingma scholar-saint Dropugpa.