Abstract: Microorganisms play a significant role in the formation process of rural black and odorous water bodies. It is of great significance to fully understand their community structure and functional characteristics in order to clarify the mechanism of black and odorous water formation and implement effective governance measures. To this end, a total of 29 rural black and odorous water bodies, including pit-pond type and ditch type, in Jiaozhou City, Pingdu City, and Laixi City were studied. The water quality characteristics and black odor levels in different types of water bodies were analyzed. Based on the 16S rRNA high-throughput sequencing, the microbial community characteristics of the water bodies and their response relationship with the water quality characteristics were described, and the ecological functions of microbial communities were predicted. The results showed that the average values of ammonia nitrogen (NH₃-N), dissolved oxygen (DO), and transparency were 17.4 mg/L, 5.63 mg/L, 13.9 cm and 9.3 mg/L, 6.25 mg/L, 15.5 cm in the water bodies of the pit-pond type and the ditch type, respectively, and the degree of black and odorous was higher in the former type. Microorganisms of the two types were dominated by chemoenergetic heterotrophs, and the diversity of the microbial community was greater in the pit-pond type. As a dominant phylum, the average relative abundance of phylum Firmicutes in pit-pond type water bodies was 32.10% higher than that of 18.29% in ditch type water bodies, while as a dominant class, the class γ-Proteobacteria had an average relative abundance of 27.86% in pit-pond type water bodies lower than that of 42.74% in ditch type water bodies, and there was not much difference in the relative abundance of Psychrobacter and Flavobacterium as dominant genera in the two types of water bodies. NH₃-N and DO concentrations were significantly correlated (P<0.05) with the dominant genera of the two types of water bodies, which were the key factors influencing the microbial community characteristics. FAPROTAX predictions indicated that aerobic metabolism of organic matter and urea decomposition fermentation were the main functions of microbial communities in typical rural black and odorous water bodies in the region, and a higher nitrogen metabolism potential was found in the pit-pond type.