In order to analyze the composition and distribution characteristics of potential pathogenic bacterial communities in water and sediment and provide basic data for the prevention and control of pathogenic bacteria in Hanjiang River, samples were collected from 7 monitoring sections of Hanjiang River in spring and autumn of 2014. Based on 16S rRNA Illumina MiSeq high-throughput sequencing technology, FAPROTAX software was used to predict the pathogenic bacteria communities, 6 categories of pathogenic bacteria were identified, belonging to 6 phyla, 9 classes, 22 orders, 45 families, 105 genera. The results showed that Proteobacteria was the main component species of pathogenic bacteria community in Hanjiang River, accounting for 96.56%, Methylopumilus and Roseomonas were dominant species at the genus level. Diversity analysis showed that pathogens were more abundant in sediment than those in surface water, and there were more apparent differences between different seasons in the plankton community. Environmental factorsrelated analysis indicated that benthic communities were more sensitive to environmental factors. Zero model analysis revealed that random processes dominated the establishment ofpathogenic bacteria communities in surface water and sediment. In summary, high-throughput sequencing technology can comprehensively and deeply present microbial community information and has great potential in the detection of pathogenic bacteria.