In the present study, the abundance and phylogenetic diversity of free-living and particle-associated Verrucomicrobia were investigated in a mesotrophic lake by quantitative PCR and sequencing of the 16S rRNA gene. The relative verrucomicrobial 16S rRNA gene abundance accounted for 0.02% to 1.98% of the particle-associated bacteria and 0.52% to 1.64% of the free-living bacteria. In total, 71 operational taxonomic units (OTUs) (n = 303 clones) were identified for particle-associated bacteria, and 59 OTUs (n = 292 clones) were identified for the free-living fraction. This study determined six new putative freshwater Verrucomicrobia clusters. Of these newly defined clusters, two were exclusively represented by particle-associated bacteria (FukuS27, BourFIV). The freshwater Verrucomicrobia clusters CRE-PA29, FukuN18 and CL120-10 appeared to be dominant, comprising 22.3%, 16.15% and 14.61% of the total retrieved OTUs, respectively. The seasonal dynamics of phytoplankton communities resulted in changes in the distinct bacterial phylotypes for both the particle-associated and free-living verrucomicrobial communities. According to canonical correspondence analysis, the diversity of the particle-associated verrucomicrobial communities appeared to be primarily influenced by phytoplankton richness, rotifer abundance and inorganic nutrients, whereas the free-living fraction was correlated with the biomass dynamics of some phytoplankton classes (Chlorophyceae, Chrysophaceae, Desmidiaceae and Zygnemataceae).