The following information is copied from the website of the Jonang Foundation and their Jonangpa.com blog. It contains most of the information in these pages, as well as much information that is not found here. For a very quick overview, see their FAQ. See also the external links below.
A distinct tradition founded by Kunpang Thukje Tsondru, named after the location where it established itself, the valley of Jomonang in Central Tibet. It produced such outstanding masters as Dolpopa Sherab Gyaltsen, Jonang Chogle Namgyal, Jetsun Kunga Drolchog and Jonang Taranatha, as well as many others. Thought distinct by many, especially western scholars, the Jonangpa are anything but that. They are alive and well and have flourished greatly in the far eastern areas of Tibet, particularly in Amdo and Golok. Despite many difficulties, both in former as well as modern times, they have managed to maintain their tradition in an unbroken manner and must therefore be regarded as the 5th living tradition of Tibetan Buddhism.
In many places one finds the erroneous information, that Yumowa Mikyo Dorje was the founder of the Jonangpa. In fact he wasn't and it is doubtful that he even heard the word "Jonang" in his life. However, Yumowa is an important early forefather of this school insofar as he expressed much the same views about emptiness and ultimate reality as did Dolpopa considerably later. In Yumowa's few remaining writings however the term zhentong is not found at all. It was Dolpopa who was to formulate this doctrinal view explicitly.
After the passing away of Jetsun Taranatha in the mid-17th century, the Jonangpa became a target for political and territorial power-struggles in U-Tsang, Central Tibet. With surmounting factional rivalries and divided allegiances amongst Jonang and Geluk patrons and the Mongol Army's solidifying of Geluk power, Jonang political and territorial influence began to wane. As Mongol military might enthroned and endorsed the 5th Dalai Lama (1617-1682), and the Geluk political administration ruled, the Jonang were forced out of Central Tibet.
In the year 1650, the 5th Dalai Lama sealed and banned the study of zhentong, prohibiting the printing of Jonang zhentong texts throughout Tibet. Then in 1658, the 5th Dalai Lama forcibly converted Jonang Takten Damcho Ling (Phuntsok Choling) Monastery into a Geluk Monastery — officially initiating the demise of the Jonangpa in U-Tsang.
Although the sphere of Geluk political and military influence reached to the borders of Central Tibet, it did not penetrate the far northeastern domain of Amdo, Tibet. Here, in the remote valleys and vast countrysides of the Dzamthang, Golok and Ngawa regions, the Jonangpa took refuge and made their home.
Beginning in the year 1425 with the establishment of Choje Monastery by Jonang Chogle Namgyal's disciple Ratnashri (1350-1435), the Jonangpa have lived in the Dzamthang and surrounding counties of Amdo. Under the imperial patronage of the Ming Court of China, the Jonangpa were able to thrive. In fact, by the mid-16th century, the Jonangpa had consolidated their monastic complexes within the Dzamthang area in Amdo to the extent that they were the local imperial regents. This is where the Jonangpa later gathered during their 17th century Geluk persecution. Surviving outside the range of Geluk influence, the Jonangpa have been building monasteries and transmitting their vital teachings on zhentong and the Kalachakra Tantra ever since.
In the 18th century two masters, Kathok Rigdzin Tsewang Norbu (1698-1755) and the 8th Tai Situpa Chokyi Jungne (1700-1774), became instrumental in reviving the interest in and spread of Jonangpa practices and teachings, particularly those of the zhentong view, both in Central Tibet as well as in Kham. With the late 19th century luminaries such as Jamgon Kongtrul (1813-1899) and Jamyang Khyentse Wangpo (1820-1892), the Rime or eclectic movement was born in Kham, Eastern Tibet. Sparked by the writings and compilations of these figures, including Kongtrul's Five Treasures, there was the occasion for a re-kindling of interest in the Jonang tradition and zhentong literature.
Inspiring many of the great masters from Kham at this time such as Dza Patrul Rinpoche and Jamgon Mipham, the Jonang Kalachakra perfection process practices and distinctive zhentong view gained attention from other traditions as well. Meanwhile this period continued to produce some of the greatest masters of contemporary Jonang thought up through the late 20th century, including Bamda Thubten Gelek Gyatso (1844-1904) and Khenpo Ngawang Lodro Drakpa (1920-1975).
In the 1960's, many of the great living exemplars of the Jonang were forced out of their monasteries, and they fled into the countryside of Amdo where they wandered as nomads or took shelter in caves as yogis. Over the next two decades, the Jonangpa lived without homes in their homeland, gathering during the summer for their annual rains-retreat in order to continue to transmit their lineage. After the Cultural Revolution in 1976, the Jonangpa began returning to their monasteries where they have been rebuilding monasteries and reviving their unique spiritual tradition up to today.
Presently there are more than 40 Jonang monasteries in the Amdo and Golok regions of northeastern Tibet, and many more small mountain retreats.
The Jonangpa have just begun to make an appearance outside of Tibet. There is a small Jonang monastery in Shimla, northern India, and another one just recently established in Kathmandu, Nepal near the great Boudanath stupa. Apart from that, there are a few centers in the west, mainly the "Dorje Ling" centers in the U.S. as well as the "Tibetan Buddhist Rime Institute" in Australia.
For a probably incomplete list of present-day Jonangpa monasteries in Amdo and Golok, see Jonang monasteries.