Abstract: 6 genetic distances (D_A, D_C, D_S, D_sw,（σμ）² and D_TL) and 2 cluster methods (UPGMA and NJ) were used to evaluate the reliabilities of construction of phylogenetic trees based on the microsatellite data from 6 cattle populations in bovine subfamily in China. The results showed that the reliabilities of construction of phylogenetic trees were affected significantly by the heterozygosity of microsatellite sites. D_A and D_C genetic distances showed generally higher reliability than other distances to obtain correct phylogenetic tree, but we can’t confirm which is better to obtain the correct phylogenetic tree for NJ and UPGMA. D_TL genetic distance needed to be improved to construct the phylogenetic tree. Finally, usefulness and limitations were discussed to construct of phylogenetic trees from microsatellites.