This study examined the possible effects of banana cultivation on phytoplankton biomass and community structure in southwest China along the Lancang-Mekong River. Water and phytoplankton samples were collected on March (dry season) and August (rainy season), and physical-chemical properties of water, phytoplankton biomass and community structure were determined. The results indicated that the banana cultivation resulted in increases in sediment, total phosphorus (TP) and total nitrogen (TN) concentrations at estuaries of Lancang-Mekong River branches. Cultivation decreased phytoplankton diversity, abundance and biomass, as well as changed the phytoplankton community structure at estuaries of branches. Sediment concentration (increased by cultivation) was considered as the dominant influence factor of phytoplankton biomass and community structure. However, at downstream sites (primary channel), banana cultivation did not cause (result from its huge flow) the significant changes in physical-chemical properties of water, phytoplankton biomass or community structure.