The present research provides detailed information on the geographic and bathymetric distributional patterns of fishes and describes the main species assemblages of the continental shelf and upper slope off El Salvador. The sampling was based on 673 bottom-trawl tows taken during research surveys from April to November 2003. The data analysis was based on presence-absence matrixes and was conducted with PRIMER 6 software. A total of 148 fish species were recorded during the study period: the families with the highest number of species were Sciaenidae (13) and Carangidae (10), and the highest percentages of occurrence were registered for Porichthys margaritatus (40.6%), Pontinus sp. (34.8%) and Monolene dubiosa (33.1%). The cluster analysis by depth showed three faunistic associations: (1) on the inner and part of the mid continental shelf (20-60 m), (2) one bathymetric stratum on the mid continental shelf (80-100 m), and (3) on the outer continental shelf and upper slope (120-240 m). The cluster analysis by geographic zones showed separation between three zones: Western, Central and Eastern Zones off El Salvador. The Central zone is characterized by a different fish community of mixed habitat, while the main factor that determined the fish assemblages on the continental shelf and upper slope was depth.