This study investigates the genetic diversity and ethnohistory of four Central Anatolian settlements from a local perspective to better understand the complex population history of Anatolia. The objectives of this project are to (1) document the biological and cultural diversity in contemporary settlements in the Yuksekyer region, (2) describe the population history of the Yuksekyer settlements within an ethnohistorical context, and (3) contextualize the findings of broader studies, which address major population events, such as the Neolithic expansion and the Turkic invasion, from a local perspective. To accomplish these goals, ethnohistorical fieldwork was conducted using interviews and questionnaires to obtain genealogical information about participants and record the local histories of these settlements, including their cultural and social affinities with each other. During this process, biological samples were also collected from the Yuksekyer inhabitants for genetic analysis. These samples were screened for mtDNA, Y-chromosome, and autosomal polymorphisms, and the resulting data analyzed with statistic and phylogenetic methods to define the biological affinities of Central Anatolian populations, and reconstruct the migration history of the region. The ethnohistorical information obtained through fieldwork facilitated a more thorough historical and cultural understanding of genetic variation in Turkey than has been achieved in previous studies. Furthermore, by working at the local level, it was possible to distinguish patterns of diversity resulting from long-term inhabitation versus those arising from recent immigration into the region. The results of this study revealed that in the village level, the paternal genetic diversity was strongly structured among settlements due to patrilocality. In contrast, maternal genetic diversity is distributed more homogenously. The signatures of Turkic invasion, the Caucasus origins of a particular settlement and recent migrations were all evident in different settlements within Yuksekyer. On the national level, a reassessment of previous genetic studies of Turkish populations indicated that these studies suffer from major sampling bias. Overall, this study emphasizes the value of ethnohistorically contextualized sampling with a multi-allelic genetic analysis to obtain a more complex understanding of the study populations and better delineate the patterns of genetic history in Anatolia.