Abstract: To evaluate the status of aquatic invertebrate resources and provide a basis for genetic monitoring of species resources for the sustainable development of fisheries in the Sanmen bay, Zhejiang province, in this study the restriction site-associated DNA sequencing (2b-RAD) technique was used to analyze the genetic structure and genetic diversity of seven dominant invertebrates (Parapenaeopsis hardwickii, Oratosquilla oratoria, Exopalaemon carinicauda, Portunus trituberculatus, Sepiella maindroni, Turritella terebra bacillum and Crassostrea sikmea) in this bay. In this investigation, 12336～108139 SNP sites were obtained in 7 species, and the proportion of variant sites was 0.168%～1.571%. The results of genetic analysis showed that the average nucleotide diversity (Pi) of the seven species was 0.147～0.306, the observed heterozygosity (Ho) was 0.142～0.289, and the polymorphism information content (PIC) was 0.124～0.234. The average genetic distance was 0.118～0.246. This study showed that among the 7 representative invertebrates in the Sanmen Bay, the proportion of biological population variation sites was low, and the population genetic diversity was low. Moreover, the genetic differentiation among individuals of the same population was small. Combined with the survey of fishery resources in the Sanmen bay, the above results may be related to artificial enhancement and releasing.