Conservation and genetic improvement of cattle breeds requires the information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in Korean peninsula. Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breed pairs were evaluated with Nei’s genetic distance and Weir & Cockerham’s FST. Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds ranging from 0.25 to 0.30, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while for the other breeds -0.018 ~ -0.118. Principle component analysis analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local and exotic cattle breeds, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38, whereas for Hanwoo it was 209 in the recent 13 generation ago. This study indicates an alarming trend of reducing effective population size in Jeju Black cattle. Thus, a sustainable breeding policy should be implemented to increase the population for the genetic improvement and future conservation.