In order to study the phytoplankton community structure in mangrove forests in tropical areas and to explore the key water quality influencing factors. The samples were collected and analyzed from Qinglan Harbor of Hainan Province in November 2015, March 2016, and August 2016, respectively. The main conclusions are as follows: 7 species of phytoplankton and 74 genera(species)were identified during the investigation. 13 genera(Species)of phytoplankton, 3(genera)species of Phyllosticta, Chlorella 13 genera(species), Cryptophyta 4 genera(species), Ophiopogon 3(species), Chlorella 3 genera(species), Golden algae 3 genera(species). The dominant species of the Bamen Bay are Chaetoceros and Cyclotella sp. ; the dominant species of the mangrove intertidal zone are Pseudoanabaena sp. Alpystis, Microcystis and Chroomonas placiodea; and the dominant species of aquaculture water are Microcystis, and Chroomonas placiodea. The density of phytoplankton is the highest, followed by the Bamen Bay and the intertidal zone. Except in March, the order of the biodiversity index from high to low is: Intertidal zone, Octopus, and aquaculture water. Nitrogen was a limiting factor for algae growth in November 2015, and the one for most water bodies were phosphorus in March and August. Algae are mainly related to nitrogen and phosphorus nutrients and metal ions, and seasonal changes have no obvious effect on their relationship.