Algae are main primary producers in streams and rivers, and they can be classified as planktonic or periphytic algae based on their living forms. In the same river, planktonic and periphytic algae mainly live in different habitats, where they may transform each other through settling or resuspension and compete for important resources. Comparing spatio-temporal patterns of lotic planktonic and periphytic algae and their relationships with environmental factors may be helpful for us to understand correlations between these two types of algal assemblages. However, such research is still limited. In this study, we surveyed planktonic and periphytic algae and physico-chemical variables from the upper reaches of the Jinsha River in the autumn of 2019 and the summer of 2020. We compared seasonal differences in community structures of planktonic and periphytic algae by using Non-metric Multidimensional Scaling (NMDS) and Permutational multivariate analysis of variance (PERMANOVA) and identified physico-chemical variables that were important to algal patterns by using BIO-ENV analysis and Mantel test. We found that both planktonic and periphytic algal assemblages were dominated by diatoms, in which Achnanthes minutissima, Fragilaria capucina and Navicula accomoda were dominant in planktonic algae, and Achnanthes minutissima, Cocconeis placentula, and Gomphonema olivaceum were dominant in periphytic algae. The average densities of planktonic and periphytic algae in the autumn were 2.41×10⁵ ind./L and 9.43×10³ ind./cm², respectively, which were significantly higher than those in the summer (4.84×10⁴ ind./L, 4.84×10³ ind./cm²). Although both types of algae exhibited significantly seasonal differences in community compositions, only periphytic algae had significantly seasonal differences in richness. The physical and chemical variables that significantly correlated with planktonic algal assemblages kept relatively consistent between seasons, including total nitrogen, ammonia nitrogen and elevation. In contrast, environmental driving forces for periphytic algal patterns were seasonal-specific with elevation and silicate in the autumn, and total nitrogen, pH and chemical oxygen demand in the summer. Correlation between periphytic algal assemblages and physico-chemical variables was higher in both seasons when compared with that of planktonic algae. Meanwhile, the geographical distance also had significant effects on spatial patterns of algal assemblages. However, when geographic effects were controlled, community patterns of both types of algae were only significantly related to environmental distance in the summer. Our study highlights associations and differences between lotic planktonic and periphytic algal assemblages. Base on the finding that periphytic algae had more significantly seasonal dynamic and were more sensitive to environmental changes, we suggested that periphytic algae might be used as routine bio-indicators for monitoring and assessing of ecological conditions of streams and rivers.