[Objective]The aim was to prove that the mitochondrial genes of Cyt b and 12S rRNA with different evolutional rates have effects on the topological structures of phylogenetic trees.[Method]The complete sequences of Cyt b and 12S rRNA from 15 species in 12 families of snakes were downloaded and extracted from GenBank,while their molecular phylogenetic trees were constructed by Maximum Likelihood（ML） method with GTR ＋I ＋G substitute model based on PAUP4.0 software.[Result]With the same software,methods and species,the difference in topological structures of phylogenetic trees was mainly due to different evolutional rates of Cyt b and 12S rRNA genes.[Conclusion]In studies on phylogenetic trees,aimed to different research species and purposes,phylogenetic trees should be constructed by choosing the correct and appropriate genes.
