According to recent historical findings, Kyrgyz history dates back to 201 BC. The early Kyrgyz lived in the upper Yenisey River valley, central Siberia (see Yenisei Kirghiz for details). Chinese and Muslim sources of the 7th–12th centuries AD describe the Kyrgyz as red-haired with fair complexion and green (blue) eyes. First appearing in Chinese records of the Grand Historian as Gekun or Jiankun (鬲昆 or 隔昆), and later as part of the Tiele tribes, they were once under the rule of Göktürks and Uyghurs. The descent of the Kyrgyz from the autochthonous Siberian population is confirmed on the other hand by the recent genetic studies (The Eurasian Heartland: A continental perspective on Y-chromosome diversity).
Remarkably, 63% of the modern Kyrgyz men share Haplogroup R1a1 (Y-DNA) with Tajiks (64%), Ukrainians (54%), Poles (56%) and even Icelanders (25%). Haplogroup R1a1 (Y-DNA) is believed to be a marker of the Proto-Indo-European language speakers.Kyrgyz genesis legend tells about an ancestor and father of all Kyrgyzes Kyzyl Taigan (Red Dog). A daughter of the khan was in the habit to take long walks in a company of 40 maidens-servants. Once, on return home after her usual walk, the Princess saw that her native aul was ravaged by an enemy. In the aul they found only one alive creature, a red dog. The princess and her 40 maids become mothers, in a company with only one male attraction, a red dog. By the number of matrons, the posterity of 40 maidens, kyrk-kyz, began to be called Kyrgyz people.   The cult of the Heavenly Dog was widespread between the tribes west and east of the ancient China. 
The Kyrgyz state reached its greatest expansion after defeating the Uyghur Khaganate in 840 AD. Then Kyrgyz quickly moved as far as as the Tian Shan range and maintained their dominance over this territory for about 200 years. In the 12th century, however, the Kyrgyz domination had shrunk to the Altay Range and the Sayan Mountains as a result of the rising Mongol expansion. With the rise of the Mongol Empire in the 13th century, the Kyrgyz migrated south.
Various Turkic peoples ruled them until 1685, when they came under the control of the Oirats (Dzungars).