This study aimed to describe the distribution and relative abundance of the phytoplankton obtained during the two seasons (rainy and dry seasons) from the Red river system. The water and phytoplankton samples were monthly collected during the year 2012 at four sampling stations along the Red River (Yen Bai, Vu Quang Hoa Binh, and Ha Noi) . Environmental variables (e.g. temperature, dissolved oxygen, pH, suspended solids, conductivity, TDS, NO3-N, NH4-N, PO4-P, Total Phosphorus; and DOC) and phytoplankton (e.g. cell density and relative abundant species) were analyzed. Six phytoplankton classes were identified with the Bacillariophyceae dominating in the phytoplankton community. A distinct seasonal variation in phytoplankton structure was observed with high cells density in dry season and low values in rainy season. PCA (Principal Component Analysis) showed that suspended solid factor that governed the temporal and spatial distribution of phytoplankton structure in the Red River system.