Abstract:The structure, species composition and seasonal dynamics of benthic diatom assemblages in two kinds of wetland, mangrove and reed wetland, in Qi’ao Island, Zhuhai were investigated from March 2007 to January 2008. Samples of surface sediment layer (5 cm) were collected and detected under microscope. There were 113 taxa benthic diatom belonging to 28 genera, of which 95 taxa in mangrove and 42 taxa in reed wetland. Abundance of benthic diatoms ranged from 14.3 to 553.5 cells cm-3. The diversity indices and evenness index varied greatly in different sites and sampling time, but those in mangrove were higher than those in reed wetland. Species composition significantly differed in the two sites. Pennales, such as species from Gyrosigma, Pleurosigma and Pinnularia were dominant in the mangrove, while Centrales dominated in the reed wetland, such as Cyclotella and Coscinodiscus. Analysis of similarity indicated that the effects of site sediment were more important than that of season.