In this study, we conducted morphological and molecular analyses of Perinereis wilsoni, a species being considered for aquaculture in China. We found this species difficult to identify because of its close morphological similarity to the sympatric P. mictodonta and thus sought genetic markers to more easily distinguish it and to investigate its phylogenetic relationship to P. mictodonta and other nereidids. For the first time, we sequenced, assembled, and annotated the complete mitochondrial genome, nuclear ribosomal sequences (18S-ITS1-5.8S-ITS2-28S), and four nuclear histone genes (H3-H2A-H2B-H4) of P. wilsoni. Comprehensive bioinformatics methods were employed to assemble the genome-skimming data of P. wilsoni to ensure assembly quality. Phylogenetic analyses based on five datasets of the available mitochondrial genomes (32 taxa in Nereididae, including 8 taxa in Perinereis), using maximum likelihood and Bayesian analyses, provide support for the monophyly of the genus Perinereis. In contrast, the P. nuntia species group, a subgroup within Perinereis, is nonmonophyletic. Perinereis wilsoni has a closer phylogenetic relationship with P. vancaurica and P. nuntia. Our study serves as a baseline for future work on the cultivation, reproductive biology, and phylogeny of P. wilsoni.