Abstract: This study analyzed the bacterial diversity of pond water and sediment in three different culture systems of yellow catfish (Pelteobagrus fulvidraco) using Illumina Miseq. Three culture systems are yellow catfish monoculture system, yellow catfish/grass carp polyculture system, and yellow catfish/grass carp/silver carp/bighead carp polyculture system. The results showed that 41256 to 77508 sequences were read from each sample, a total of 655100 16S rDNA sequences were generated, and then these sequences were clustered into 608—3686 OTUs with 97% similarity. According to α-typed diversity indices, the abundance and diversity of microbial communities of the final water samples were higher than those of the initial water samples for all three culture systems. The yellow catfish/grass carp polyculture system has the highest microbial community abundance (Chao1index: 2199.25, ACE index: 2374.60). The yellow catfish/grass carp/silver carp/bighead carp polyculture system has the highest microbial community diversity (Shannon index: 4.88, Simpson index: 0.021). The cluster analysis and principal co-ordinates analysis showed that yellow catfish monoculture system and yellow catfish/grass carp polyculture system are highly similar in microbial composition and community structure. A total of 8 phyla were identified in all 12 samples, and Proteobacteria was the dominant group in all samples. Actinobacteria increased at the end and became the second dominant group, especially in yellow catfish/grass carp polyculture system (37.6%). Bacteroidetes increased in yellow catfish monoculture system in the later periods (1.96% to 10.98%). There were differences in the composition of microorganisms at the genetic level in all samples. Aeromonas dominated in the water samples of yellow catfish monoculture system in the end periods (5.81%). This study revealed that yellow catfish/grass carp/silver carp/bighead carp polyculture system is a promising culture system from the perspective of microbial community structure and diversity.