In this work we describe by the first time the microfaunal content (foraminifers and ostracods) of the benthos of the Basque continental shelf, by studying the spatial distributions of benthic foraminifer and ostracod assemblages in relation to the environmental parameters affecting the sediments of this region of the Bay of Biscay. Most abundant benthic foraminifer species in the surface samples are Brizalina spathulata, Bulimina marginata, Cassidulina laevigata, Hyalinea balthica, Lobatula lobatula, Rosalina globularis, Textularia sagittula and Uvigerina peregrina. Most abundant and widespread ostracod species are Lindisfarnia guttata, Costa edwardsii and Pterygocythereis ceratoptera-jonesi group. Multivariate analyses (Cluster Q, R; DCA) of samples and species of these organisms have been performed to provide an accurate description of these distributions. Based on these analyses six different facies are characterised in this shelf, according to their microfaunal content as well as to the average values of environmental parameters (CaCO 3, POC, silt–clay and hypoxic biological markers). Of these facies, the eastern fringe and the mudpatch have a more pronounced hypoxic character relative to the western facies in this shelf. Results provided by benthic foraminifer and ostracod assemblages totally agree and indicate their dependence of the environmental parameters of the sediment. In the eastern area the influence of deeper waters has been detected, probably as upwelling through the canyons, evidenced by the occurrence of bathyal species of foraminifers ( Fontbotia wuellerstorfi, Hoeglundina elegans) and ostracods ( Krithe spp., Cytheropteron spp., Buntonia spp.). The noticeable oil-affection found in benthic specimens, very likely caused by the oil-spill of the “Prestige” in the benthonic environment of the Basque continental shelf, has been detected eight months after the spill. Despite the studied bathymetric range of 50 to 150 m, the depth interval of specimens affected by oil-spill is that of the outer shelf (93–150 m). Benthic microfauna evidence oil-pollution in the bottom sediments and demonstrate a wider affected area in the bottom of the Basque shelf than previously stated.