Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of , the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll concentrations (>0.5 μg/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll concentrations. Higher chlorophyll concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication. One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll concentrations, we know little about how changes in seawater chlorophyll concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.