The spread of pathogenic bacteria in marine environments poses significant risks to human health and threatens the stability of marine ecosystems. However, little is known about the dynamics of these pathogens during seasonal hypoxia in coastal waters. This study investigates the community structure and temporal changes of pathogenic bacteria in the central Bohai Sea from May to August 2017, using high-throughput 16S rRNA gene sequencing. Pathogenic bacteria were detected in all samples, comprising 0.13% to 24.65% of the total prokaryotic sequences. Notably, the abundance of certain pathogenic genera, especially Vibrio and Arcobacter, increased significantly under hypoxic conditions, particularly in August. Environmental factors, including dissolved oxygen (DO), salinity, ammonia, phosphate, silicate, and chlorophyll a (Chl a), were identified as key drivers of these changes in pathogenic bacterial communities. Redundancy analysis (RDA) indicated that the vertical distribution of pathogenic bacteria was closely related to variations in DO and nutrient concentrations. In August, a clear separation was observed between the pathogenic communities in the surface and hypoxic zones, with the hypoxic regions showing a higher abundance of pathogenic bacteria. Additionally, the stability of the pathogenic community increased from May to August, suggesting a persistent threat to the central Bohai Sea as hypoxic zones develop. These findings highlight the potential intensification of health risks as oxygen-depleted areas expand, with a growing prevalence of pathogenic bacteria that may pose serious risks to coastal populations. This study offers new insights into the ecological behavior of pathogenic bacteria in aquatic systems and provides critical information for the development of effective strategies to mitigate the spread of pathogens in coastal environments.