Abstract: The Futian National Mangrove Nature Reserve in Guangdong, the only national-level natural reserve located in the urban hinterland in China, is best for studying the impact of human activities on the mangrove ecosystem. The phytoplankton community is an important indicator group for studying the health status of the aquatic ecosystem. In recent years, with the implementation of Shenzhen's water treatment and pollution control actions, the health status of the mangrove aquatic ecosystem needs further study. In September 2023, we carried out an investigation and analysis on the phytoplankton in Futian mangroves and environmental factors. The results indicate that the water quality in the Futian Mangrove Nature Reserve was classified as Class III, showing a state of moderate eutrophication. A total of 122 planktonic plant species were identified, with densities ranging from 0.02×10⁶ to 122.21×10⁶ cells·L⁻¹ (1.04±3.05)×10⁷ cells·L⁻¹ on average and biomass from 18.04 to 999.71 μg·L⁻¹ (264.93±292.49) μg·L⁻¹ on average. The majority of dominant species were indicative of meso-eutrophic conditions or were types that preferred water bodies rich in organic matter, reflecting that the survey waters still exhibit a certain degree of eutrophication. Significant differences in planktonic community structure were observed between mangrove forests and surrounding fish ponds. The pH, electrical conductivity and salinity were identified as key environmental factors influencing planktonic community abundance, biomass, and diversity in the survey area. In general, the aquatic ecological environment in the Futian Mangrove Reserve needs further improvement.