Abstract: Objective To identify Aeromonas at species level by using rpoD and gyrA gene, compare the identification results and get more accurate classifications of 187 strains in this study. Methods PCR amplification and sequencing were conducted for rpoD and gyrA gene of 187 strains of Aeromonas identified by biochemical method, the phylogenetic tree was constructed by using the sequencing results and the specific reference sequences. Results By rpoD gene sequence analysis, 187 stains were classified into 7 species, however, by gyrA gene analysis, 9 species were identified and 1 was unspecified, and the top three species were consistent with the results of rpoD gene analysis, namely, A.veronii bv. sobria, A. caviae and A. aquariorum. The two added species were A. allosaccharophila and A.jandaei. Among the Aeromonas strains identified, 174 (93%) had consistent identification results by using the two genes except 13 strains (7%). Conclusion The detections of rpoD and gyrA genes can identify most Aeromonas strains, however, the detection of housekeeping genes is necessary to identify the strains which cannot be identified in rpoD and gyrA detection.