During a series of blooms of Noctiluca scintillans and Mesodinium rubrum, we applied high-throughput sequencing of the 16S rRNA gene to investigate the population dynamics of free-living (FL) and particle-attached (PA) bacteria, in an attempt to evaluate the influence of protozoan bloom-induced disturbance on the structuring of these two communities. Our findings revealed that FL and PA bacterial community compositions (BCCs) displayed distinct profiles during the sequential blooms, and the PA flora responded more dynamically to these pulse perturbations. The dominant bacterial groups (e.g., Flavobacteriaceae, Rhodobacteraceae, Vibrioneceae, and SAR11 subclade ï¿? in these two communities displayed different levels of connectivity with the bloom causative species and the environmental factors. In addition, more FL bacteria groups were associated with M. rubrum, while more PA bacteria groups related to N. scintillans. Potential endocytic bacteria of N. scintillans, particularly Vibrioneceae and Rickettsiaceae, opportunistically thrived at the peak of the bloom, suggesting that they could be important players influencing the dynamic and biogeochemical cycling of the blooms. Overall, disparities in the substrate preference and thermal niche of various bacteria taxa, as well as the short duration of the blooms (1-3 days), contributed to the diverse responses of the FL and PA bacterial communities to these protozoan blooms. Our research provides an insight into the responses of FL and PA bacterial communities to the blooms caused by protozoa like N. scintillans and M. rubrum, and highlights the ecological significance of certain keystone bacteria groups during this kind of cosmopolitan protozoan blooms.