Harmful algal blooms (HABs) of Cochlodinium polykrikoides exert pressure on nutritional resources; however, little is known about how they affect bacterial diversity. To investigate this, 110 water samples were collected from the Southern Sea of South Korea. Samples were divided into three groups based on environmental factors and phytoplankton data with a similarity of 85% using non-metric multidimensional scaling. Group I represented high-severity blooms and had a mean C. polykrikoides abundance of 1,560 cells mL. Groups II and III represented low-severity blooms, with mean densities of 68 and 57 cells mL, respectively. Inorganic nitrogen and phosphorous and dissolved organic carbon concentrations increased with C. polykrikoides density. This may reflect the change in biogeochemical cycling due to HAB release of extra polymeric substances. Furthermore, a total of 88 core bacterial operational taxonomic units (OTUs, with relative abundance > 1%) were identified. These included Gammaproteobacteria (36 OTUs), Flavobacteriia (24), Alphaproteobacteria (18), and other taxa (11). In Group I, the relative abundances of Gammaproteobacteria and Alphaproteobacteria were higher, and the relative abundance of Flavobacteriia was lower compared those in Groups II and III. Functional analysis based on the core bacterial OTUs revealed that chemoheterotrophy-related functions were more common in Group I than in Groups II and III. OTU #030, which was selected as strong indicator species, was strongly positive correlated with C. polykrikoides abundance (r = 0.95). Our results demonstrate that there are complex interactions between HABs, environmental factors, and core bacteria and functions, which could have important implications for biogeochemical cycling.