A comparative study for abundance, biomass and diversity was carried out for the prokaryote, meiofauna and macrofauna communities at three depth stations (1200, 1800 and 2100 m) along the Malta Escarpment (Mediterranean Sea). Our investigation showed a two-fold increase with depth in prokaryote abundance; the contribution of prokaryote biomass to the total benthic biomass was predominant at all depths. Bacteria were the dominant prokaryote component and Archaea formed a considerable fraction (20%-30%) of the prokaryote assemblages. The meio- and macrofauna abundances and meiofauna biomass did not decrease significantly with depth but macrofauna biomass did. The α diversity did not follow a clear bathymetric trend for both nematode and macrofauna species. Probably because of the large number of eurybathic nematode genera, nor did the turnover diversity in nematode composition change down the depth gradient. Conversely, for the macrofauna there was a perceptible change in community composition between the shallowest station and the two deeper stations. Food availability affected only the macrobenthic component. The increase in the prokaryote organisms with depth and the dominance of nematodes and macrofauna deposit feeders suggest active grazing by the two benthic components on microbes. This would transfer energy to the higher trophic levels through the microbial compartment.