Recently, the human activities including economic growth and urbanization posed serious environmental health risks to the Jiulong River Watershed (JRW). In order to gain a full understanding of the distribution of potential pathogenic bacteria (PPB) in this area, we used 16S rRNA amplicon pyrosequencing technology to investigate planktonic and benthic bacterial community in two main tributaries (North River, NR, and West River, WR) of the Jiulong River (JR). At the genus level, a total of 68 genera of PPB were identified in JR, which accounted for 6. 1% of total gene sequences. Clostridium, Mycobacterium and Sphingomonas were three most dominant genera, which accounted for 54. 5% , 5.9% and 5. 6% of the total gene sequences respectively, and occurred in all samples. At the species level, a total of 48 species of PPB were identified in JR, which accounted for 0.76% of total gene sequences. Afipia felis, Mycobacterium asiaticum, Clostridium baratii, Brucella melitensis and Delftia tsuruhatensis were the five most dominant species, and accounted for 48.9% , 20.3% , 8% , 2.7% and 1.7% , respectively. Statistical analysis indicated that the number of taxa (species or genera) of PPB in JR water samples were significantly more than those from JR sediment samples. Moreover, WR water samples harbored the most abundant and diverse of PPB, suggesting that WR water might have a high potential risk for pathogen contamination. In addition, statistical analysis indicated that the diversity and abundance of PPB (species or genera) are significantly positively correlated with nutrient (nitrogen and phosphorus) concentrations, suggesting that human activities in the JRW such as sewage discharge from livestock and wastewater treatment facilities play important roles on affecting the distribution of PPB in JR. Therefore, in order to protect the public health, more efforts are needed to prevent water contamination, and conduct the real-time monitoring of PPB in JR.