Fluorescent in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to compare the community structures of free-living and aggregated bacteria at thawing period in Lake Baikal. Targeted groups were Eubacteria, $alpha$-, $eta$-, $gamma$- proteobacteria groups, Cytophaga-Flavobacterium group and Planctomycetales. Total bacterial numbers of free-living bacteria were ranged from $0.2{ imes}10^6cells{cdot}ml^-1$ to $3.2{ imes}10^6cells{cdot}ml^-1$, which were decreasing with depth, while the aggregated bacterial numbers were dramatically increasing from $0.4{ imes}10^4 to 3.3{ imes}10^4 cells{cdot}ml^-1$ with depth. The ratios of EUB probe binding cells to DAPI counts were ranged from 52.3 to 74.1% in free-living bacteria, and from 39.6 to 66.7% in the aggregated bacteria, respectively. Community structures of the aggregated bacteria were very different from each free-living bacteria at every depth. At 25 m depth, where the chlorophyll a concentration was highest, both structures were quite different from those of surface layers, rendering the fact that the community structures might be affected by phytoplankton. The vertical profile of community structure of aggregated bacteria is particular. The proportion of $eta$-proteobacteria group was increasing with depth and it was 51.8% at 100 m, but the dominant group was $gamma$-pro-teobacteria group at 250 m. Taken together, the biodiversity and succession of aggregated bacteria are quite different from free-living bacteria.