Bacteria in marine ecosystems are a morphologically, genetically and functionally diverse group. The seasonal dynamic of bacterial communities in the South and North Adriatic offshore waters and in the Krka river estuary was determined by using a combination of 454 pyrosequencing of the 16S rRNA gene and catalyzed reporter deposition-fluorescence in situ hybridization. Bacterial richness and community structure were strongly influenced by hydrological conditions in all the studied areas. A strong, deep winter mixing of the water column and Levantine intermediate water ingression in the South Adriatic, seasonal environmental conditions and the Po river flow in the North Adriatic and the river flow coupled with a strong salinity gradient in the Krka river estuary had a pronounced impact on bacterial communities. Members of the SAR11 clade were dominating the prokaryotic picoplankton communities in the Adriatic Sea with maximal abundances in the oligotrophic area of the South Adriatic. Betaproteobacteria were mainly appearing in ecosystems under the influence of riverine waters. Members of the phylum Actinobacteria were present in all the studied areas but high abundances with a pronounced seasonality were detected only in the riverine waters of the Krka estuary. Marine groups NS4 and NS5 belonging to the phylum Bacteroidetes together with the gammaproteobacterial SAR86 clade were identified to cooccur with phytoplankton blooms in all the studies areas. Typical marine cyanobacteria, Synechococcus and Prochlorococcus, were dominating the cyanobacterial communities in the Adriatic. Synechococcus was dominating the cyanobacterial communities in the North Adriatic while Prochlorococcus was mainly constrained to the South Adriatic. The Deep Adriatic Sea was characterized by typical bacterial deep ocean clades: SAR324, SAR202 and SAR406. In addition, a higher abundance of Archaea was found in this deep part of the Adriatic Sea