The composition and structure of sublittoral faunal assemblages inhabiting soft bottoms (15–72 m depth) within the Marine Protected Area ‘Acantilados y Fondos Marinos de Calahonda-Castell de Ferro’ in southern Spain (North Alboran Sea, Mediterranean) have been studied in relation to sediment and water column variables. Three assemblages were identified and corresponded to mixed bottom, unstable bottom and coastal detritic bottom assemblages, based on Pérès & Picard's (1964) benthic classification. A total of 14,318 individuals were collected and 218 species identified, molluscs being the best represented group (141 species). Species richness displayed significant differences with depth and transect, with the highest values observed in the medium to very fine sand and muddy bottoms with bioclasts located at the shallowest sampling stations. The presence of some rare and poorly known invertebrates that are scarce in other areas of the Mediterranean Sea is remarkable, such as the crustacean decapods Bythocaris cosmetops and Pagurus mbizi, Atlantic species with no records in the Mediterranean Sea, and the bathyal molluscs Poromya granulata and Alvania testae, collected at shallow depths. The spatial distribution of faunal assemblages was mainly related to depth and percentage of gravel and clay according to the canonical correspondence analysis. The geographic location of the area, the heterogeneity of soft bottoms and the presence of upwellings in the area may favour the high biodiversity found in the studied soft bottoms. This study increases the scarce knowledge of the circalittoral fauna of sedimentary habitats of the Alboran Sea, providing a baseline for the management of this interesting SCI and for the EU Marine Strategy Framework Directive.