Abstract: In order to create an indigenous DNA metabarcoding database for zooplankton in the Zhoushan sea area and support the research on species identification, phylogenetic relationships, and genetic analysis of marine zooplankton, we compiled a list of zooplankton species in the Zhoushan sea area based on data collected over the past 14 years. We downloaded a total of 195 mitochondrial cytochrome oxidase subunit I (COI) barcode sequences and 134 small ribosomal subunit 18S rRNA barcode sequences from the NCBI GenBank database. Then we calculated the intra-and interspecific genetic distances of copepod species. The results show that the average interspecific genetic distance of the COI gene was 0.3136, which was 34.09 times as high as the average distance within each copepod species. Likewise, the average interspecific genetic distance for the 18S rRNA gene was 0.2628, which was 26.82 times as high as the average intraspecific distance. The DNA barcode of the COI gene exhibited a clear barcoding gap, while there were overlaps between the intra-and interspecific genetic distances based on the 18S rRNA gene. The phylogenetic tree constructed using COI and 18S rRNA genes demonstrates that both genes can distinguish different zooplankton taxa at the order and family levels effectively. This DNA barcoding database will facilitate species identification and biodiversity assessment of zooplankton, providing valuable references for evaluating the marine environment in the Zhoushan sea area.