The aim of the present study was to perform genetic diversity and population structure estimation on 382 individuals from seven Chinese Tibetan ecotype yak population using twenty-one microsatellites. The results revealed that the HO ranged from 0.4854±0.0194 in NNV to 0.6086±0.0267 in YRY, and the NA ranged from 3.86±1.98 in XMY to 6.05±3.37 in NNV. The least number of markers which deviated from Hardy-Weinberg equilibrium within the population was W, and largest number of deviations was in the NNV population. Consistent of phylogenetic relationships between the seven populations was identified by Phylogenetic N-J network (Reynold’s genetic distance), FST and Principal components factor (PCA) analysis. These analyses inferred that the population cluster data was not only consistent with the populations’ geographic habits but could also be influenced by artificial selection and feeding style. Lastly, two credible genetic backgrounds were identified from the yak populations in this study using STRUCTURE software, which corresponded to previous knowledge about different molecular genetic markers. Therefore, unexpectedly, our study indicated that the diversity of some of the populations was decreased, leaving us to improve and refine our conversional strategy. In addition, this resulted in a greater understanding of human yak phylogenetic differentiation as well as providing data support for understanding the evolution and migration of yak population in future studies.