Borjigids recovered.
Batumöngke Dayan Khan and his khatun Mandukhai reunited the entire Mongol nation under the Genghisids in the early 16th century. In the mid-16th century, Altan Khan of the Tümed, a grandson of Dayan Khan – but no legitimate Khan himself – became powerful. He founded Hohhot in 1557 and his meeting with the Dalai Lama in 1578 sparked the second introduction of Tibetan Buddhism to Mongolia. Abtai Khan of the Khalkha converted to Buddhism and founded the Erdene Zuu monastery in 1585. His grandson Zanabazar became the first Jebtsundamba Khutughtu in 1640.
The last Mongol Khan was Ligden Khan in the early 17th century. He got into conflicts with the Manchus over the looting of Chinese cities, and managed to alienate most Mongol tribes. He died in 1634 on his way to Tibet, in an attempt to evade the Manchus and destroy the Yellow Hat sect of Buddhism. By 1636, most Inner Mongolian tribes had submitted to the Manchus, who founded the Qing Dynasty. The Khalkha eventually submitted to Qing rule in 1691, thus bringing all of today's Mongolia under Beijing's rule. After several wars, the Dzungars (the western Mongols or Oirats) were virtually annihilated during the Qing conquest of Dzungaria in 1757–58. Some scholars estimate that about 80% of the 600,000 or more Dzungars were destroyed by a combination of disease and warfare. Outer Mongolia was given relative autonomy, being administered by the hereditary Genghisid khanates of Tusheet Khan, Setsen Khan, Zasagt Khan and Sain Noyon Khan. The Jebtsundamba Khutuktu of Mongolia had immense de-facto authority. The Manchus also forbade mass Chinese immigration, allowing the Mongols to keep their culture.
Until 1911, the Qing Dynasty maintained control of Mongolia with a series of alliances and intermarriages, as well as military and economic measures. Ambans, Manchu "high officials", were installed in Khüree, Uliastai, and Khovd, and the country was subdivided into ever more feudal
