Univariate diversity indices and multivariate analyses (cluster and multidimensional scaling (MDS) were performed in order to evaluate biodiversity in two neighbouring areas of the Eastern Mediterranean with different fishing intensity. Data were collected from two trawl surveys (July and August 2000) in two areas of the Ionian Sea. In the area off the South-eastern Italian coast, there is a trawl fishery at depths between 300 and 700 m that targets the deep-sea shrimps Aristeus antennatus and Aristaeomorpha foliacea. In the other area off Northern Greece, fishing is only carried out down to 400 m depth.While diversity indices did not show convincing differences in the community structure between the two study areas considered as a whole, the multivariate analysis showed a clear pattern linked to depths and areas highlighting the distribution of abundance of the various species. Depth played the main role in the group differentiation, indicating the existence of two quite distinct bathyal faunal assemblages: one on the upper slope, the other on the middle slope. The results of the geographic characterization of the diversity and of the assemblage composition are discussed considering the different fishing intensity as well as the environmental conditions in the two areas of the same basin.