Abstract: With the largest sea area in the South China Sea, Xisha Islands are rich in marine resources. To understand the composition and distribution characteristics of zooplankton in this area, a comprehensive survey of 14 stations in Xisha Islands was conducted in May 2019. Morphological methods and metabarcoding methods based on 18S V9 sequencing was used to examine the composition of zooplankton samples. We found that the main zooplankton species in Xisha Islands were copepods, Malacostraca and Sagittoidea, of them the relative abundance was both high by morphological and molecular identification. The average zooplankton density in the 14 stations was 707.53±378.34 ind/m³ while it varied with zooplankton abundance, species composition and dominant species among the stations. Compared with morphological identification (86 species from 11 phylum, 17 classes, 18 orders), many more species were obtained by 18S V9 identification (233 OTUs from 22 phylum, 46 classes, 85 orders) and the relative abundance of representative categories and diversity index showed significant correlation with morphological identification in most stations, indicating that the metabarcoding technique and morphological identification method have good comparability in the evaluation of species diversity, and metabarcoding technique exhibited high application potential in efficient assessment of marine biodiversity. However, due to molecular methodology for zooplankton species identification is still in its infant stage, the relevant database is still not complete, and a variety of methods are still needed for the accuracy diversity assessment of zooplankton.