Flavobacterium species belong to phylum Bacteriodetes and are a group of microorganisms that are environmental or pathogenic to fish. Members of this group are abundant in both marine and freshwater environments and tolerate a wide range in salinity. Successful immigration from freshwater to the brackish northern Baltic Sea has been observed. The phylogenetic study of bacterioplankton in the central Baltic Sea revealed, that genus Flavobacterium is the second richest group representing ~10% of all sequence fragments belonging to the phylum Bacteroidetes. Evidence for distribution patterns of distinct flavobacterial clades, however, is sparse. Current project will provide for better understanding of the physiology and diversity of both environmental and pathogenic representatives of the genus Flavobacterium in salinity and organic matter gradients. An integrated phylogenetic approach to assess and interpret the diversity will be used. The strategy relies on large-scale screening and quantification for Flavobacterium DNA as well as sequencing of target bacteria in Baltic Sea. Experimental approach will reveal the competitive abilities as well as morphological flexibility of Flavobacterium bacteria in different nutrient and labile carbon gradients and grazing pressure by zooplankton.