Benthic metazoa and stained foraminifera (>32 μm) were studied in relation to prevailing environmental parameters in the Aegean Sea (Sporades Basin and Cretan Sea) and Levantine Basin (Ierapetra Basin) during the METEOR Cruise 40 Leg 3 (December 1997–January 1998). The sampling stations differed in nutrient contents, which were indicative of the oligotrophy of the eastern Mediterranean Sea. Meiobenthic abundance decreased significantly with depth and the total standing stock in the top 6 cm sediment layer was significantly higher at the northern stations (204-231 ind./10 cm2). In the abyssal Ierapetra Basin, the abundance for all meiobenthic taxa was minimal (10-26 ind./10 cm2). Nematodes and foraminifera were dominant and accounted together for 79-93% of the total abundance. All taxa were concentrated near the surface of the sediment and only nematodes showed a deeper penetration into the sediments in the Sporades Basin. Concentrations of chloroplastic pigments, total organic carbon and total organic nitrogen were higher in the Sporades and Ierapetra Basins than in the Cretan Sea, reflecting: (a) the different productivity levels and, thus, the higher food availability in the former than in the latter; (b) the seasonal accumulation of organic matter from the euphotic zone down to the abyssal trenches; and (c) the transportation of large amounts of sediment and organic matter in the Sporades and Ierapetra Basins, which are located at the mouth of submarine canyons, through riverine inputs, flush flooding, sediment failure and dense shelf water cascading. Meiofaunal abundances in the Aegean Sea were positively correlated with chlorophyll a, phaeopigments and chloroplastic pigment equivalent (CPE), and were not correlated with any of the remaining sediment descriptors, thus indicating the dependence of meiofauna on food availability.