In order to study eukaryotic plankton community succession,and the relationship between eukaryotic plankton community and physicochemical factors in the ponds with Carassius auratus gibelio in coastal mud flat,water samples were collected monthly in 2011.We measured the relevant physicochemical factors,analyzed the diversity of eukaryotic plankton community by 18s rDNA PCR-DGGE technique,and analyzed the relationship between the plankton community and physicochemical factors by canonical correspondence analysis(CCA)method.The results showed that the concentration of total phosphorus(TP)ranged from 0.17 to 1.12 mg/L all the year round,and presented its peak value in July.The range of phosphate(PO₄-P)concentration was from 0.04 to 0.30 mg/L,and the peak values occurred in July and August.The range of nitrite(NO₂-N),ammonia-nitrogen(NH₄⁺-N)and nitrate(NO₃-N)concentration was 0.02-0.57 mg/L,0.20-2.37 mg/L,0.04-10.47 mg/L,and their peak values occurred in December,May and November,respectively.DGGE profiles of 18S rRNA gene fragments from the pond revealed that the diversity of eukaryotic plankton assemblages was highly variable.A total of 73 observable bands were amplified from January to December,and the average was 24.67.Shannon-Wiener index of pond was higher in May,June,August and September.The cluster analysis(UPGMA)dendrograms of eukaryotic plankton revealed remarkable seasonality except for March,July and November.August,September and October clustered into one group.April,May and June clustered into one group,and January,February,December clustered into one group.CCA revealed that temperature,total phosphorus and ammonia-nitrogen played a key role in the structure of the eukaryotic plankton community in pond,which can provide a theoretical basis for ecological regulation of aquaculture and optimization of aquaculture model.DGGE method was a cost-effective way to gain insight into seasonal dynamics of eukaryotic plankton communities in culture ponds.