Abstract: To understand the variation characteristics of phytoplankton population structure in the polyculture ponds of Scylla serrata and Penaeus monodon, we have conducted a monthly survey on the phytoplankton in three cultured ponds in Panyu District, Guangzhou from March to November 2018, and discussed the relationship between phytoplankton and environment factors based on redundancy analysis (RDA). The results show that a total of 29 species in five Phyla were identified, among which the most abundant group was Bacillariophyta, with 19 species accounting for 65.5% of the total species, followed by Cyanophyta (5 species, 17.2%), Pyrrophyta (3 species), Chlorophyta (1 species) and Euglenophyta (1 species). Navicula directa, Nitzschia delicatissima, Gyrosigma acuminatum, Ceratium macroceros and Oscillatoria tenuis were the dominant species during the investigation. The abundance of phytoplankton cells varied from 2.56×10³ to 189.2×10³ cells·m⁻³. The variation of Shannon-Weaver diversity index ranged from 0.468 to 2.597. RDA reveals that nutrients, salinity and pH were the primary environmental factors influencing phytoplankton community.