The fauna of molluscs associated with deep subtidal Zostera marina beds (12-16 m) in southern Spain (Alboran Sea) has been characterised in terms of micro-habitat preference, feeding guilds and biogeographical affinity. The species list (162 taxa) is based on sampling completed before the strong eelgrass decline experienced in 2005-2006, using different methods (small Agassiz trawl covering 222 m2 and quadrates covering 0.06 m2) and different temporal scales (months, day/night). Dominant epifaunal species are Jujubinus striatus, Rissoa spp. and Smaragdia viridis in the leaf stratum and Nassarius pygmaeus, Bittium reticulatum and Calliostoma planatum on the sediment. Nevertheless, the infauna dominated the epifauna in terms of number of individuals, including mainly bivalves (Tellina distorta, T. fabula, Dosinia lupinus). The epifauna of both the sediment and leaf strata included high numbers of species, probably due to the soft transition between vegetated and unvegetated areas. The dominant feeding guilds were deposit feeders, filter feeders and peryphiton grazers, but ectoparasites (eulimids), seagrass grazers (Smaragdia viridis) and an egg feeder (Mitrella minor) also occurred, unlike in other eelgrass beds of Europe. The molluscan fauna of these Z. marina beds is essentially derived from the local fauna, which includes many widely distributed species along European coasts, with a low representation of strictly Mediterranean or strictly Atlantic species. This fauna is richer than that found in other eelgrass beds of Europe, and deserves important attention for conservation.