Abstract: In order to construct the molecular identification method of Perinereis aibuhitensis based on Cytb gene, by taking Perinereis aibuhitensis cultured in coastal Fujian as the test material, the mitochondrial Cytb gene sequences of Perinereis aibuhitensis were obtained by using DNA sequencing and its molecular identification was carried out. Furthermore, the neighbor-joining method (NJ method) in Mega4 software was used to construct the phylogenetic tree of Cytb genes in the subfamily. The results showed that after sequencing and Blast aligning of PCR amplified products of Perinereis aibuhitensis, the Cytb gene sequence length of Perinereis aibuhitensis was 349 bp, which was 97%-99% similar to Perinereis aibuhitensis in NCBI database, but was not similar to other species of nereid. In the phylogenetic tree of subfamily sericulaceae, Perinereis aibuhitensis and Perinereis nuntia came together first, and then they were together with Platynereis; Nereis and cheilonereis came together, and so did Paraleonnates and Neanthes Kinberg. The results preliminarily confirmed that the mitochondrial Cytb gene sequence could be used for the molecular identification of Perinereis aibuhitensis.