In this study, the concept of functional groups was applied for the first time to the seasonal dynamics of the phytoplankton community of Mudanjiang River (northeast China). The environmental variables as well as the phytoplankton communities were determined in 2007. The river showed strong seasonal fluctuations in water physical and chemical condition. A total of 11 phytoplankton functional groups (C, D, E, J, MP, P, T, T B , W1, X2 and Y) were identified that included 30 species. Groups C (Asterionella formosa and Cyclotella meneghiniana), MP (Cocconeis placentula, Cymatopleara solea, Diatoma vulgare, Ochromonas fragilis, Pinnularia major and Ulothrix variabilis), P (Fragilaria capucina, Fragilaris sp., Aulacoseira granulate and Aulacoseira granulate var. angustissima), T B (Aulacoseira varians and Navicula exigua, Navicula radiosa), X2 (Chlamydomonas sp.) and Y (Chroomonas acuta, Cryptomonas ovata, and Cryptomonas sp.) were the dominant groups during the study period. Mudanjiang River phytoplankton functional groups exhibited a noticeable seasonality in which group Y was predominant in the winter and spring associated with greater soluble reactive phosphorus availability, group MP in the summer associated with ammonium-nitrogen availability, and group P in autumn associated with greater transparency. This study underscores the usefulness of functional groups in studying phytoplankton dynamics in this river, in which phytoplankton dynamics can be significantly affected by tourism.