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This study focuses on the community structure of aggregated bacteria in Lake Baikal and relationships with free-living bacteria.Fluorescent in situ hybridization (FISH) methods were used in samples of bacteria taken in April, 2001. Bacterial counts of free-living ranged from 52.3 to 74.1% in free-living bacteria and from 39.6 to 66.7% in aggregated bacteria, respectively. Community composition of aggregated bacteria was very different from free-living bacteria, especially at 25m depth where highest phytoplankton numbers were observed. The vertical profile of aggregated bacteria community was very characteristic. Beta-Proteobacteria increased with depth down to 100m. At 250m, gamma-Proteobacteria was 44% of DAPI bound cells, while other groups were less than 1%. We conclude that community structures of free-living and aggregated bacteria were different, and they may sustain the ecosystem in independent ways.