Abstract: [Objective] Because abundant fossil evidences of Equus animals were discovered, it has become the best example of species evolution. However, there are still other troublesome issues in fossil evidences,such as the gaps in the fossil record and difficulty to distinguish from each other. The aim of this study was to provide some understandings for the genetic differentiation and genetic relationship identification of Equus animals at molecular level, provide some helps for the protection, exploitation and utilization of Equus animals and provide basic teaching materials for the teaching of biology. [Method] The molecular biology softwares were used to align the mitochondrial DNA（mtDNA）sequences in GenBank. Single nucleotide polymorphism（SNP）sites were detected. And the phylogenetic analysis based on SNPs was conducted. [Result] Abundant genetic variations were found in three mitochondrial genes（COX1, Cytb and ND4）, which could reveal the genetic relationship of Equus animals.[Conclusion] The topological structures of the constructed phylogenetic trees based on the three genes were basically the same. In the three trees, white rhinoceros sequences were all placed as the outgroup. And Przewalskii horse sequence was clustered with horse sequence firstly. Then the three kind of Asian wild ass were clustered. All zebra sequences were clustered firstly and then they were clustered with the donkey sequence.