Abstract: Using the information from 12 microsatellite to estimate Level of genetic differentiation、gene flow and genetic structure of three indigenous cattle populations (Luxi, Bohai and Minnan) and two reference cattle populations (chinese Holstein and Qinhai yak) in China. The global heterozygote deficit across of all populations (Fis) amounted to 58.5% (P<0.001). The overall significant (P<0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 43.2%. The five cattle populations were highly differentiated (Fst= 26.9%, p<0.001) with all loci. The heterozygote deficit within population (Fis) was highest in Luxi cattle and lowest in Yak. The average number of effective migrants exchanged per generation (Nem) was highest (1.149) between Luxi and Holstein, and lowest (0.509) between Luxi and Yak. With the application of prior population information, cluster analysis achieved posterior probabilities from 91.4% to 98.5% of correctly assigning individuals to their rightful populations. Combining the information of cluster analysis, gene flow and STRUCTURE analysis, five cattle populations belong to three genetic clusters, a taurine (Luxi and chinese Holstein), a zebu (Bohai and Minnan) and a yak cluster. This indicate that Bohai black have more blood of the Bos indicus than Luxi cattle. The evolution and development of three indigenous cattle populations were discussed in this article.