Abstract: This study investigated the community structure and seasonal variation of phytoplankton and periphyton on different substrates (macrophytes, stone and sediment), and analyzed the relationships between planktonic and periphy-tic filamentous algae and their interactions with environmental factors in the western littoral zone of West Lake from December, 2014 to August, 2015, and also discussed the cause of seasonal outbreak of filamentous algal bloom during the process of the ecological restoration. The results showed that bacillariophyta has occupied the first place (52.5%, 60.4%, 86.7% and 72.7%, respectively) among the algal species of different habitats (phytoplankton, epiphyton, epipelon and epilithon), and that Cyanophyta (10.1%, 8.9%, 6.7% and 15.2%, respectively) and Chlorophyta (26.3%, 19.8%, 5.6% and 10.6%, respectively) came second and third, and that of others were relatively low. The composition and seasonal pattern of dominant species of phytoplankton and periphyton on different substrates were quite different. The density of filamentous algae on macrophytes was significantly higher than that on sediment and stone. Moreover, a significant positive correlation was found between filamentous algae in planktonic habitat and on Myriophyllum. This suggest that the filamentous algae on Myriophyllum might be one of vital sources in planktonic habitat. The correlation analysis elucidated that periphytic algae and filamentous algae had no significant correlation with all physical and chemical factors monitored (water depth, transparency, dissolved oxygen, water temperature, pH, total nitrogen, solu-ble reactive phosphorus, total phosphorus, etc.). These results provide reference for the control of abnormal proliferation of filamentous algae in the West Lake.