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The Jonangpa or Jonang school of Tibetan Buddhism was founded in the early 14th century by Sherab Gyeltsen, a monk trained in the Sakyapa school. The Jonangpa school was thought to have become extinct in the late 17th century at the hands of the Fifth Dalai Lama who forcibly annexed the Jonangpa monasteries to his Gelugpa school. Recently, however, Tibetologists were surprised to discover that some remote Jonangpa monasteries actually escaped this fate and have continued practicing uninterrupted to this day. As many as 5000 monks may be members of the remnant Jonangpa school practicing in areas at the edge of historic Gelugpa influence.
In the early 14th century the monk Sherab Gyeltsen broke away from the Sakyapa school and established the Jonangpa school at Jonan about a 160 km northwest of the Tashilhumpo monastery in Shigatse. There the Jonangpa built a large monastery and constructed a printing press.
The Jonangpa school had generated a number of renowned Buddhist scholars, the greatest of whom was Taranatha (1575-1634). Taranatha placed great emphasis on the Kalachakra system of tantra which became an important part of Gelugpa teaching after the Gelugpa absorbed the Jonangpa monasteries. Taranatha's influence on Gelugpa thinking continues even to this day in the teaching of the present 14th Dalai Lama who actively promotes initiation into Kalachakra.
After several centuries of independence, however, in the late 17th century the Jonangpa order came under the attack by the Great Fifth Dalai Lama who forcibly converted their monasteries to the Gelugpa order.
While the Gelugpa embraced the Jonangpa teaching on the Kalachakra, they ultimately opposed the Jonangpa for another set of teachings. Sherab Gyeltsen, the founder of the Jonangpa, and subsequent lamas had developed a teaching known as Mind Only which held that enlightenment could be obtained by the cessation of all thoughts. This teaching was closely related to the teachings of medieval Chan Buddhism in China (which also gave rise to Zen Buddhism in Japan). This association with Chinese Buddhism tainted the Jonangpa in the eyes of the Gelugpa who considered the true teachings to derive from the Indian saints, particularly Atisha. An additional motivation in criticizing the Jonangpa sect as Zen-followers was it enabled the Gelugpa to lay claim to the high moral ground previously held only by the rival Nyingmapa sect who were proud of their ancient and unsullied transmission from the Indian saints (and not being sullied by later transmissions as where the Sakyapa, Kagyupa, and Gelugpa).
Modern historians have identified two other reasons which likely led the Gelugpa to suppress the Jonangpa:
First, the Jonangpa taught that large gifts of property to monasteries did not help one achieve enlightenment. This undercut the financial practices of the Gelugpa who were growing rapidly through exactly those means at the time.
Second, and more significantly, the Jonangpa had political ties that were very vexing to the Gelugpa. The Jonangpa, along with the Kagyupa, were historical allies with the powerful house of Zanabazar the son of Prince Tosiyetu Khan, ruler of the Khan Uula district of Outer Mongolia. Tosiyetu and his son were of Khalkha lineage, meaning they had the birth authority to become Khan. When the young boy was declared the spiritual leader of all of Mongolia, suddenly the Gelugpa were faced with the possibility of war with the former military superpower of Asia. While the Mongol Empire was long passed its zenith, this was nonetheless a frightening prospect and the Dalai Lama sought the first possible moment of Mongol distraction to take control of the Jonangpa monasteries.
In accordance with the observation that "victors write history" the Jonangpa were until recently thought to be an extinct heretical sect. Thus modern Tibetologists were astonished when fieldwork turned up several active Jonangpa monasteries, including the main monastery called Tsangwa located in Dzamthang County, Sichuan, China. Almost 40 monasteries, comprising about 5000 monks, have been subsequently been found, including in the Amdo and Gyarong districts of Qinghai and the Tibet Autonomous Region. Presumably these remnant survived because they were far from the Gelugpa capital at Lhasa and closer to sympathetic powers in Qing Dynasty China.