Abstract: Jianghan Plain is an alluvial plain located in the middle and south of Hubei province, China. In order to explore the community structure of phytoplankton in an integrated rice-crayfish symbiosis farming (IRCSF) system, algal species, cell density, algal biomass, and physicochemical factors in four rice-crayfish symbiosis farming water bodies were monthly investigated in the Jianghan Plain from April 2016 to December 2016. There were 124 species belonged to 7 phylum, which observed in this integrated system; 78 species belonged to Chlorophyta; 16 species belonged to Cyanophyta; 15 species belonged to Bacillariophyta; 3 species belonged to Euglenophyta; 2 species belonged to Cryptophyta; 7 species belonged to Pyrrophyta; and 3 species belonged to Chrysophyta. The number of algal species, cell density value, and chlorophyll-a content all reached the maximum value from June to September, while the minimum value appeared in December. Algal cell density fluctuated in the range of 1.37×10⁵ to 2.93×10⁸ cells/L, and the content of chlorophyll-a varied from 0.15 to 208.60 μg/L. During the study period, 28 dominant species were totally identified. The dominant species were Oscillatoria, Dactyloccocpsis, Microcystis, Chlorella, and Cryptomonas. The annual variation of the Shannon-Wiener diversity index was from 0.64 to 6.3. The maximum value of diversity index achieved in October, while the minimum value was in August. The results showed that the community structure of phytoplankton in the IRCSF sytem was complex with an obvious spatio-temporal heterogeneity. Since algae plays an important role in water environment and crayfish cultivation, it is of great significance to pay attention to the change of community structure of phytoplankton in the IRCSF system.