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Actinobacteriaare highly abundant in pelagic freshwater habitats and also occur in estuarine environments such as the Baltic Sea. Because of gradients in salinity and other environmental variables estuaries offer natural systems for examining factors that determineActinobacteriadistribution. We studied abundance and community structure ofBacteriaandActinobacteriaalong two transects in the northern Baltic Sea. Quantitative (CARD-FISH) and qualitative (DGGE and clone libraries) analyses of community composition were compared with environmental parameters.Actinobacteriaaccounted for 22–27% of all bacteria and the abundance changed with temperature. Analysis of 549 actinobacterial 16S rRNA sequences from four clone libraries revealed a dominance of the freshwater clustersacI andacIV, and two new subclusters (acI-B scB-5 andacIV-E) were assigned. WhereasacI was present at all stations, occurrence ofacII andacIV differed between stations and was related to dissolved organic carbon (DOC) and chlorophylla(Chla) respectively. The prevalence of theacI-A andacI-B subclusters changed in relation to total phosphorus (Tot-P) and Chlarespectively. Community structure ofBacteriaandActinobacteriadiffered between the river station and all other stations, responding to differences in DOC, Chlaand bacterial production. In contrast, the composition of activeActinobacteria(analysis based on reversely transcribed RNA) changed in relation to salinity and Tot-P. Our study suggests an important ecological role ofActinobacteriain the brackish northern Baltic Sea. It highlights the need to address dynamics at the cluster or subcluster phylogenetic levels to gain insights into the factors regulating distribution and composition ofActinobacteriain aquatic environments.