A mat-forming population of the giant sulfur bacterium Thiomargarita was discovered at the flank of the mud volcano Amon on the Nile Deep Sea Fan in the Eastern Mediterranean Sea. All cells were of a spherical and vacuolated phenotype and internally stored globules of elemental sulfur. With a diameter of 24-65μm, Thiomargarita cells from the Eastern Mediterranean were substantially smaller than cells of previously described populations. A 16S rRNA gene fragment was amplified and could be assigned to the Thiomargarita-resembling cells by fluorescence in situ hybridization. This sequence is monophyletic with published Thiomargarita sequences but sequence similarities are only about 94%, indicating a distinct diversification. In the investigated habitat, highly dynamic conditions favour Thiomargarita species over other sulfur-oxidizing bacteria. In contrast to Thiomargarita namibiensis populations, which rely on periodic resuspension from sulfidic sediment into the oxygenated water column, Thiomargarita cells at the Amon mud volcano seem to remain stationary at the sediment surface while environmental conditions change around them due to periodic brine flow. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.