The distribution of ester-linked phospholipid fatty acid (PLFA) in sediments of 12 sampling stations located in the German Bight, Skagerrak/northern Kattegat, Frisian Front, Oyster Ground, eastern North Sea and the Dogger Bank area was studied to compare the in situ microbial community structure of depositional and non-depositional sites. A total of 36 fatty acids in the range of C 12 to C 24 were determined. They consisted of saturated, branched, monounsaturated, polyunsaturated and hydroxy fatty acids, and variation was revealed in the relative proportions (mol %) of these fatty acids. The distribution of specific fatty acids was significantly different between depositional and non-depositional sites. Additionally, we could discriminate communities of sites which are intermediate in sedimentation regime. Highest total PLFA content was found at depositional sites. The PLFA profiles of all sites were dominated by bacteria, with highest bacterial contribution to the sedimentary PLFA pool at depositional sites. A high proportion of aerobic prokaryotes (up to 40%) at depositional sites indicated the occurrence of aerobic microniches in the corresponding anoxic sediments. Bacterial groups being a component of the degradation pathways of complex macromolecules (e.g. Cytophaga and Actinomycetes) were found in significant higher abundances at depositional sites compared to the other sites. At depositional sites, sulphate-reducing bacteria (SRB) (e.g. Desulfobacter spp.) were more abundant compared to the other stations. The relative contribution of microeukaryotes to the sedimentary PLFA pool was significantly higher at depositional sites. A nutritionally limited benthic system at non-depositional sites in the offshore is indicated by a microbial community exposed to higher physiological stress than those of the organically enriched sediments of the depositional sites.