This dissertation explores the genetic histories of several populations living in the Altai Republic of Russia. It employs an approach combining methods from population genetics and phylogeography to characterize genetic diversity in these populations, and places the results in a molecular anthropological context. Previously, researchers used anthropological, historical, ethnographic and linguistic evidence to categorize the indigenous inhabitants of the Altai into two groups – northern and southern Altaians. Genetic data obtained in this study were therefore used to determine whether these anthropological groupings resulted from historical processes involving different source populations, and if the observed geographical and anthropological separation between northern and southern Altaians also represented a genetic boundary between them. These comparisons were made by examining mitochondrial DNA (mtDNA) coding region single nucleotide polymorphisms (SNPs), control region sequences (including HVS1), and several complete mitochondrial genomes. Variation in the non-recombining portion of the Y-chromosome (NRY) was characterized with biallelic markers and short tandem repeat (STR) haplotypes. Overall, this work provided a high-resolution data set for both unipaternally inherited genetic marker systems. The resulting data were analyzed using both population genetic and phylogeographic methods. Northern Altaians (Chelkan, Kumandin and Tubalar) were distinctive from the southern Altaians (Altai-kizhi) with both genetic systems, yet the Tubalar consistently showed evidence of admixture with southern Altaians, reflecting differences in the origin and population history of northern and southern groups as well as between ethnic northern Altaian populations. These results complement the observation of cultural differences as noted by anthropological/ethnographic research on Altaian populations. These differences likely reinforced and maintained the genetic differences between ethnic groups (i.e., a cultural barrier to genetic exchange). Therefore, biological and cultural lines of evidence suggest separate origins for northern and southern Altaians. Phylogeographic analysis of mtDNA and NRY haplotypes examined the impact of different historical events on genetic diversity in Altaians, including Neolithic expansions, the introduction of Kurgan cultures, the spread of Altaic-speakers, and the intrusion of the Mongol Empire. These insights also allowed for a greater understanding of the peopling of Siberia itself. The cultures of Altaian peoples ultimately helped to shape their current genetic variation.