The composition and structure of a molluscan assemblage was studied in a deep subtidal eelgrass bed located in southern Spain before and after the eelgrass decline experienced during 2005 and 2006 due to illegal trawling by fishermen. Sampling was undertaken in summer 2004 (with eelgrass) and summer 2007 (without eelgrass) in an extensive eelgrass bed located in Cañuelo Bay (12–14 m depth) and in the same area once the eelgrass bed disappeared. Eelgrass was completely absent in those samples of summer 2007 and an increase of the organic content and mud was registered in the sediment between 2004 and 2007. The density and the richness of molluscan species decreased significantly in summer 2007, especially for epifaunal gastropods associated with the leaf and sediment stratum. Some species disappeared completely in summer 2007 such as the dominant periphyton grazers Jujubinus striatus and Rissoa spp., the egg feeder Mitrella minor and the seagrass feeder Smaragdia viridis as well as the infaunal bivalve Solemya togata. Other species increased their densities such as the carnivores Cylichna crossei or C. cylindracea as well as the bivalve Nucula nitidosa. Some dominant infaunal species, such as Chamelea gallina, Spisula subtruncata or Tellina fabula did not significantly change their densities. The composition and structure of the assemblages in summer 2004 and summer 2007 was significantly different according to the Bray–Curtis similarity index using qualitative and quantitative data and considering the entire assemblage (epifaunal and infaunal species) or only the infaunal species. The registered changes in the molluscan assemblage may have produced cascade effects in higher trophic levels because molluscs generally represent an important food source for some decapods and fish. Urgent conservation measures are needed for protecting the remaining fragmented eelgrass beds of southern Spain from further illegal fisheries activities and other types of human impacts (e.g. sand extraction and coastal infrastructures), because they support the most diverse faunistic communities for eelgrass beds in Europe due to their bathymetry and geographical location.