Studies on the phytoplankton functional group (PFG) composition of intensive-culturing fishponds were carried out in the Pearl River Delta during the initial, mid-, and late stages of the culture period. The results showed that high phytoplankton density, algal biomass and species abundance were observed in the sampling ponds. The average phytoplankton cell density was 1.32×10⁸ cells/L, with a maximum of up to 3.00×10⁸ cells/L. The average phytoplankton biomass was 168.17 mg/L, with a maximum of up to 345.41 mg/L. A total of 196 algal species, including a few varieties and forma, were distributed among the following 8 major taxonomic categories:Chlorophyta (91), Euglenophyta (40), Bacillariophyta (27), Cyanophyta (23), Dinophyta (7), Cryptophyta (4), Xanthophyta (3), and Chrysophyta (1). The algae in the sampling ponds were identified to the following 28 PFGs:A, B, C, D, F, G, G₂, H1, J, K, L₁, LM, L₀, M, MP, N, P, S1, S2, T, T_D, W1, W2, W_S, X1, X2, X_Ph, and Y. Frequency distribution analysis showed that C, F, J, MP, N, P, W1, X2, Y, K, L₀, M, and W2 were the dominant PFGs. These PFGs showed high biomass and occurrence frequency in the sampling ponds, which indicated that the phytoplankton community structure in the culturing ponds was in a stable state with simple ecological functions. Redundancy analysis between the environmental factors and the dominant PFGs showed that organic content was the primary affecting factor, followed by nutritive materials and their proportions (including TP and N:P). Least influential were physical parameters, including transparency, pH, dissolved oxygen, total dissolvable solids, and water temperature. On the basis of the traditional biodiversity evaluation standard, the water quality of the sampling ponds was clear, but the habitats of the dominant PFGs indicated that the water was heavily polluted, which was consistent with the results of the measured parameters and water appearance. In this study, we observed that the number of PFGs in the mid-stage of culture was greater than that in the initial or late stage. This pattern was obvious in the pond, which underwent frequent water changes during the mid-stage. It was concluded that providing sufficient water changes could be an important measure for preventing water quality deterioration during the megathermal period. Furthermore, the results of the present study showed that compared with traditional biodiversity methods, the phytoplankton functional group concept could be successfully used to assess the real ecological status of phytoplankton in intensive-culturing fishponds, and also provides a method for analyzing pond ecosystems.