Abstract: To investigate the effects of Euglena blooms on phytoplankton community structure in aquaculture ponds in the Kaijiang area, Sichuan Province, water quality monitoring was conducted from April to September 2022 throughout one complete aquaculture cycle. The study examined ponds operated by Kaijiang Minsheng Fisheries Development Co., Ltd., comparing ponds experiencing Euglena blooms (bloom ponds) with those without blooms (control ponds). Phytoplankton species composition, density, and biomass were analyzed, and the relationship between phytoplankton communities and environmental factors was investigated using redundancy analysis (RDA). Results showed that 96 phytoplankton species from 6 phyla (including 11 dominant species) were identified in bloom ponds, comprising 42 species of Chlorophyta, 17 species of Bacillariophyta, 9 species of Cyanobacteria, 22 species of Euglenophyta, 2 species of Dinophyta, and 1 species of Cryptophyta. In control ponds, 137 phytoplankton species from 7 phyla (including 9 dominant species) were identified, comprising 62 species of Chlorophyta, 21 species of Bacillariophyta, 16 species of Cyanobacteria, 29 species of Euglenophyta, 2 species of Dinophyta, 1 species of Cryptophyta, and 2 species of Xanthophyta. The average phytoplankton densities ranged from 3.86×10⁷ to 1.26×10⁸ cells/L in bloom ponds and from 5.95×10⁷ to 1.35×10⁸ cells/L in control ponds. Average biomass ranged from 4.17 to 13.33 mg/L in bloom ponds and from 4.31 to 10.44 mg/L in control ponds. The Shannon-Wiener diversity index, Pielou evenness index, and Margalef richness index for phytoplankton in bloom ponds ranged from 1.316 to 1.909, 0.236 to 0.364, and 1.339 to 2.688, respectively, while in control ponds they ranged from 2.605 to 3.570, 0.554 to 0.703, and 3.924 to 5.830, respectively. Based on these three indices, bloom ponds were classified as heavily to moderately polluted, while control ponds were classified as lightly polluted to unpolluted. RDA analysis revealed that total nitrogen, total phosphorus, dissolved oxygen, permanganate index, ammonia nitrogen, and soluble phosphate were the environmental factors significantly affecting phytoplankton community structure and composition in bloom ponds. In control ponds, ammonia nitrogen, total dissolved solids, total phosphorus, nitrate nitrogen, and water temperature were the significant environmental factors. This study provides fundamental data for the prevention and control of Euglena blooms in freshwater aquaculture systems.