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Yunnan Province is believed to be one of the earliest areas in China to be occupied by human forms of the genus Homo. Anthropologists believe there were several waves of migrations of humanoids out of Africa, into what is now India and northward into Tibet, and from there eastward into what is now Yunnan. Settlements were already widespread in the area by the Neolithic or New Stone Age period.

Evidence of settlements in the Dian area near Kunming date back as far as 700 BC. By the 3rd century BC there were already many settlements around the Dian lake area. By 109 BC the area fell under the control of the Han dynasty and became part of the trade routes connecting China to Burma and India.

In 649 AD six groups combined to form the Nanzhao kingdom around Lake Dian. It expanded widely throughout Yunnan and into Burma, Laos and Thailand, then into Sichuan. 

In the year 902 the Nanzhao kingdom was overthrown. It was followed by three dynasties in quick succession. In 937 Duan Siping seized power and established the Kingdom of Dali. The kingdom continued through 22 monarchs until 1253, when it was overthrown by an invasion of the Mongol Empire. The Mongols established their capital at Dali and in 1274 created the Province of Yunnan.

The Mongols defeated many native regimes, including the Dali kingdom. The Mongols ruled Yunnan as one of the 10 provinces of their empire until they were expelled in 1368, leading to a period of chaos until 1381 when the Ming dynasty took control. 

Under the Ming dynasty Yunnan was ruled by a hereditary feudal system. When the Ming Dynasty fell in northern China, Yunnan was the last southern base of the regime. By 1681 it gave way to the Qing dynasty.

But fierce resistance to the Qing dynasty from the Muslim Hui people continued. It grew into a rebellion in 1856 with the establishment of a rebel government that called itself the Pingnan Sultanate, which declared itself independent of China. It lasted from 1856 to 1872, when the Qing dynasty put down the rebellion. During the time when Qing consolidated power in Yunnan, a large influx of migrants from Central China moved into Yunnan.

In 1911 the Qing Dynasty collapsed and Yunnan fell under the control of local warlords who financed themselves through the opium trade. Yunnan remained a frontier, remote from the center of Chinese administration.

The Chinese republic was formally established on January 1, 1912, after the Xinhai Revolution, which overthrew the Qing dynasty, ending more than 2,000 years of imperial rule in China.

On December 25, 1915, Cai E and Tang Jiyao declared the independence of Yunnan, and established the Yunnan Military Government. They gathered an army of 20,000 to for the Movement for Nation Protection or Uprising of Yunnan.

In 1919 the ideas Marxism began to spread in Yunnan. In 1927 the Communist Party of China (CPC) established a CPC Branch of Yunnan in Kunming.

During the Second Sino-Japanese War Yunnan became a haven for refugees fleeing the east, including many university professors and students. The National Southwest Associated University (known as Lianda) was established and became a major academic center, producing many noted scholars and scientists.

After the establishment of the People's Republic of China in 1949, conditions in Yunnan gradually improved as the central government consolidated its borders in the southwest to incorporate Yunnan under its administration.