Like culturally similar Altai, the steppes of Khakassia and southern Krasnoyarsk Territory were a cradle of Siberian civilisation. Standing stones and kurgany pock the landscape; many are more than 3000 years old, though the most visually impressive date from the Turkic period (6th to 12th centuries). The Khyagas (Yenisey Kyrgyz) empire, from which the name Khakassia is derived, ruled much of Central Asia and central Siberia from around AD 840 until its golden age ended abruptly with the arrival of Chinggis Khaan and company.

Russian trappers and Cossacks started moving into the northern, forested part of Krasnoyarsk Territory from the 15th century, building forts and imposing duties on indigenous fur hunters. The colonisation was spurred by the construction of the Great Siberian Trakt, a road connecting Siberia to European Russia. Colonists were supplemented by people exiled from all over the empire, most notably from Poland. By the beginning of the 20th century, the territory was largely populated by ethnic Russians, with the shamanist Khakass people largely Christianised and integrated into Russian society.