In this study, we used genetic diversity analysis with Microsatellite (MS) markers to determine the relationships between two Mongolian native breeds (MNB) (n=78) which were compared with three foreign breeds (FB) (n=110) in Mongolia. For the analysis of genetic diversity, 11 recommended MS markers from a diversity panel conducted by the ISAG / FAO or previously reported MS markers were used. A total of 392 MS alleles were identified. The mean number of alleles (MNA) per locus across population was 7.126 and the mean observed heterozygosity (HObs), expected heterozygosity (HExp), and Polymorphism information content (PIC) were 0.753, 0.745, and 0.697, respectively. The five breeds were classified into two groups (FB in the first group, MNB in the second group), according to the neighbor - joining (NJ) tree, which was based on Nei’s standart genetic distances. Both Factorial correspondence analysis (FCA), principal coordinates analysis (PCoA) showed that the Mongol (M) breed is highly distinct from the other breeds analysed. In conclusion, these results will provide useful information for the development of native Mongolian cattle breeding and individual traceability systems as well as aid in generating strategies for conservation and breeding programs for the Mongolian cattle population.