The Toktogul valley was home for the Scythian warrior tribes due to its rich nature alread in the 7-4th centuries BC. At that time, the Scythian believed in the existence of an underground world and buried the kings and prominent warriors with their household tools, slaves, horses and arms so that they can use them during their second life in the underground world. The Toktogul Valley was one of the most populated areas of Central Asia the ancient times. During the Soviet period, the archaeologist Alexandre Bernshtam began to seek and explore the tombs of the Scythian people. As a result they deducted that there was a lot of wealth in the area but the excavations only covered a small portion of the history that is now underwater.

In the 1960s, the dam Toktogul forced to stop all the archaeological exploring of all the graves that were buried under the reservoir. In the late 18th and early 19th century, the empire of Kokand had invaded the Ferghana Valley and the territory of modern Uzbekistan. To expand its territory, they began to attack the people of the Celestial Mountains (Tien Shan in Chinese). 

The conquest began with the Toktogul valley due to the status of one of the most populated valleys of Tien-Shan at that time. The invaders found themselves facing strong resistance from local people, although they had no army. Their location in the middle of Tien-Shan allowed them to defend quickly without wasting much force. Because there was only one entrance into the valley, the number of warriors did not play a big role. But finally, due to a betrayal, Toktogul residents were defeated. The original Toktogul town is also under the reservoir.