This study is based on the extraction and sequencing of the mitochondrial DNA from 132 ancient human samples from central Mongolia dating to the Neolithic, Bronze Age, Iron Age (Xiongnu) and Mongol Empire periods. The data collected were compared to mtDNA gene pools from multiple published studies of ancient and modern human populations from across Eurasia with particular focus on Eurasian steppe populations. The results of these analyses support a model of human migration showing an original eastern population on the Neolithic Mongol Steppe that admixed with a western population, which had migrated onto the eastern Eurasian steppe zone during the Neolithic. This study demonstrates western Eurasian DNA on the eastern Eurasian steppe as far as the Mongol Steppe by the Late Neolithic, and reveals a significant western component in the Bronze Age population of Central Mongolia. It supports an indigenous population as the origin of the Xiongnu, confirms that the Xiongnu had a strongly admixed mtDNA gene pool, and indicates that a significant shift towards eastern mtDNA occurred between the Xiongnu Empire and Mongol Empire periods, which has continued up to the present.