Abstract: 【Objective】 The study aimed to investigate phytoplankton community composition and species diversity in the nearshore bays of Hainan and to explore the reasons behind differences in phytoplankton diversity，providing reference for predicting red tide occurrences and improving water quality. 【Method】 Water environment samples were collected from 4 sampling stations in each of Lingshui Bay，Haiwei Bay，Qinglan Bay and Sanya Bay. The V4 variable region of the 18S rRNA gene was amplified using PCR，and the phytoplankton community composition and species diversity in the 4 nearshore bays were analyzed based on Illumina MiSeq high-throughput sequencing. Canonical correspondence analysis（CCA），Mantel test and Spearman correlation analysis were used to explore the correlation between phytoplankton community composition and environmental factors. 【Result】 A total of 542 phytoplankton OTUs were obtained through sequencing，annotated to 8 phyla，24 classes，147 genera，and 246 species. The dominant phytoplankton genera included Chaetoceros，Nitzschia，Paraphysomonas，Ciliophrys，Skeletonema，Thalassiosira，Pleurosigma and Proto-peridinium. Bacillariophyta was the dominant phylum in Lingshui Bay and Sanya Bay，with the genus Chaetoceros exhibiting the highest diversity in the phytoplankton community. In Qinglan Bay，Chlorophyta was the dominant phylum，with Nitzschia showing the highest diversity；while in Haiwei Bay，Phaeophyta was the dominant，with Paraphysomonas exhibiting the highest diversity. The Shannon index and Simpson index of the phytoplankton community in Lingshui Bay showed significant（P<0.05）or extremely significant（P<0.01）differences compared to the other 3 bays，while no significant differences（P>0.05）in diversity indexes were observed among Haiwei Bay，Qinglan Bay and Sanya Bay. The phytoplankton community composition in all 4 bays was influenced by various environmental factors，with total nitrogen， total phosphorus，conductivity，salinity and water temperature being the major environmental factors affecting phytoplankton composition. 【Conclusion】 In the phytoplankton communities of Hainan nearshore bays，Bacillariophyta has the highest species abundance. Sanya Bay exhibits the highest phytoplankton diversity，while Lingshui Bay shows the lowest diversity and poses a potential risk of red tide occurrence. Total nitrogen，total phosphorus，conductivity，salinity and water temperature are identified as the major environmental factors affecting the composition of phytoplankton communities in the nearshore bays of Hainan. Therefore，in the process of marine resource development and utilization，it is crucial to monitor water quality pollution and changes in environmental factors in real time to ensure the health and diversity of key ecological components such as phytoplankton，prevent imbalances in phytoplankton communities and ecological disasters like red tides，thereby maintaining the stability of marine ecosystems.