The analysis of ancient DNA (aDNA) in paleogenetics has become an increasingly important subject of archaeological, anthropological, biological as well as public interest. In this study, paleogenetic analyses were carried out on the human skeletal remains from a historical cemetery site in Myeongam-ri, Asan, Korea. Archaeological records show that this particular location had been used as a habitation or mortuary site as early as the Bronze Age and up until the Joseon Dynasty. Human remains of twenty individuals out of forty-nine tombs from the Goryeo to Joseon Dynasty were selected for the analysis of this study. In order to identify the genealogy of the population and traditional burial pattern of the cemetery, we conducted comparative analyses of the hyper variable regions (HVRs) in mitochondrial DNA (mtDNA) of each sample. A number of cautious steps were taken at all experimental stages in order to avoid erroneous recombination by the segmental and modern contaminations derived from the researchers. We sequenced segmental amplicons of HVRs and assigned relevant haplogroups according to the sequence polymorphism on the basis of the known mtDNA database. The result shows that diverse haplogroups were unexpectedly present in the small population group of the Myeongam-ri site. This diversity appears to be related to the geographical conditions and archaeological properties of the Myeongam-ri site.