Fluorescent in situ hybridization (FISH) with rRNA -targeted oligonucleotide probes has become one of the major techniques in environmental microbiology, allowing rapid and reliable definition of prokaryotes and quantification of population sizes. The aim was to demonstrate the applicability of the FISH method to study bacterioplankton composition in North Mamry Lake, and to follow the dynamics of two populations of common bacteria. We analyzed the phylogenetic composition of free-living bacterioplankton assemblage using oligonucleotide probes specific for Bacteria as well as for β-Proteobacteria and Cytophaga-Flavobacterium groups. Up to 53% of bacteria detected with DAPI could be detected via FISH by applying the universal bacterial probe for domain Bacteria (Eub338). Percentage of Cytophaga-Flavobacterium cluster did not exceed 20%. Members of the β–Proteobacteria appeared to be the most abundant group.