Abstract: This study analyzed the effects of dissolved oxygen content (DOC) and water temperature on the community and richness of bacteria in In-pond Raceway System (IPRS) from various viewpoints using Illumina Miseq high-throughput sequencing technology. The highest and lowest microbial richness was in September and October, respectively. In general, the microbial richness in lowest DOC was greater than that in highest DOC during the diurnal variation. The microbial richness in fecal collecting area was greater than that in aquaculture area. Proteobacteria, Actinobacteria, Bacteroidetes and Cyanobacteria were the 4 dominant species among July and November. At generic levels, Pseudomonas, Synechococcus and Flarobacterium were dominant species. Almost every bacterium had significant or extremely significant difference among different months. The richness of Pseudomonas was positively correlated to DOC (r=0.415, P<0.01), but negatively correlated to water temperature (r=–0.427, P<0.01). There was a significant correlation between Synechococcus, Cyanobacteria, CL500-29, Alpinimonas and water temperature (r=0.636, –0.448, 0.755, –0.428 respectively, P<0.01). The richness of Mycobacterium (r=0.488, P<0.01) and MNG7 were significantly correlated to DOC. Furthermore, there were significant or extremely significant relations among different bacterial communities. The microbial richness increased with the decreasing DOC level to reach peak level at 2.5 mg/L of DOC. These results suggest that stocking density, culture area, DOC, and season variety could regulate microbial richness.