The phytoplankton communities and physical and chemical factors in two types, upland pond and lowland pond, of Penaeus vannamei culture ponds were investigated. The results showed that the nutrient contents of lowland ponds were higher than that of upland ponds. Water salinity of upland ponds was higher than that of lowland ponds. Salinity may be the main factor that influenced the phytoplankton communities. Cyanophyta, such as Microcystis sp., Merismopedia glauca and Aphanizomenon flosaquae, predominated numerically in low salinity ponds, while Diatom such as Navicula cryptocephala and Asterionella formosa in high salinity ponds.