[Objectives]  To use molecular methods to identify and construct a phylogeny of three termite species; Odontotermes dimorphus Li et Xiao、Pseudocapritermes sinensis Ping et Xu and Mironasutitermes shangchengensis Wang et Li. [Methods]  Mitochondrial 16S rDNA and COⅡ partial gene sequences of the three species were amplified, sequenced and compared. After Blast and base composition analysis, sequences were submitted to the GeneBank database and neighbor-joining trees of the phylogenetic relationships between these and 10 other termites species were constructed. [Results]   The three 16S rDNA sequences are about 385 bp long, and the three COⅡ sequences are about 720 bp, long. The proportion of AT is much greater than that of CG in both genes. With respect to 16S rDNA, the minimum genetic distance and number of different nucleotides between the three focal species and the 10 other termite species termites are 0.102 and 35, whereas for COⅡ gene sequences these values are 0.024 and 16. Phylogenies based on the 16S rDNA and COⅡ sequences were consistent, but a phylogeny based on the COⅡ gene conformed more to the established taxonomic relationships between termites families and genera than that based on 16S rDNA. [Conclusion]  All three termite species can be identified on the basis of variation in 16S rDNA and COⅡ gene sequences but the COⅡ gene is more useful for phylogenetic research than the 16S rDNA gene. The most closely related species to O. dimorphus,P. sinensis and M. shangchengensis were respectively Odontotermes formosanus、Sinocapritermes mushae and Nasutitermes takasagoensis.