Abstract: 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 bacteria by DAPI staining ranged from 0.2106 to 3.2106 cellsmL-1, decreasing with depth, whereas aggregated bacterial numbers dramatically increased with depth, ranging from 0.4104 to 3.3104 cellsmL-1.Ratios of EUB probe binding cells to DAPI counts 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 bacteriawas 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.