The dynamic changes and diversity of bacterial communities in two types of ponds (M1: pond with sand around and netted bottom, M2: traditional soil pond) of Portunus trituberculatus- exopalaemon carinicauda polyculture in different seasons were investigated by the technology of terminal restriction fragment length polymorphism (T-RFLP) analysis based on bacterial 16S ribosomal RNA gene and cloning. The results showed that the bacterial communities in both M1 and M2 consisted of Proteobacteria, Bacteroidete, Actinobacteria, and Cyanobacteria. The composition of bacteria community changed dramatically with breeding time with various compositions in different ponds. The bacterial community in M1 is composed of Actinomycetes, Cyanobacterium and Proteobacteria, while the bacterial community in M2 included Cyanobacterium and proteobacteria, indicating that M1 was conducive to the growth of Cyanobacteria. The highest relative abundances of Bacteroidetes were in August and September in both M1 and M2, and M2 always has higher relative abundances of Bacteroidetes than M1 during the whole farming time. The bacterial community of M1 pond changed from high diversity index and stability structure to low diversity index and instability structure over breeding time, while bacterial community of M2 pond remained high diversity index in the late breeding time. PCA analysis showed that the seasonal variations of bacterioplankton were much more obvious in M1 than M2, indicating the greater ability of M2 to resist environmental change than M1. Correlation analysis results indicated that environmental factors have different effects on bacteria community of each pond water.