This study was conducted to elucidate the genetic relationships among native Korean cattle breeds by analyzing genetic variations and distances. Relationships among Hanwoo, Korean brindle, Korean black, Jeju black, and Holstein cattle were evaluated using 15 microsatellite markers. Korean brindle and Korean black cattle had the closest relationship based on the lowest genetic distance being observed between these breeds. A Neighbor-Net tree created using the Reynolds distances indicated that Korean brindle and black cattle formed a group separate from the Hanwoo population. However, an Fst pairwise test revealed that Hanwoo, Korean brindle, and Korean black cattle differed significantly (P <0.01). Moreover, the results of this study confirmed that Jeju black cattle became a separate established breed in Korea through a path different from that of cattle from inland regions, even though it is considered to be a Korean native breed. Overall, the results of our study indicate that Korean brindle and black cattle are indeed native Korean breeds that maintain an endangered status.