Ecological diversity based on quantitative data is widely used to characterise biological communities, but recently morphological and functional traits have also been used to analyse the structure of fish assemblages. This diversity and structure is usually linked to variables such as habitat complexity and composition, depth, and spatial and temporal variations. In this study, several fish assemblages off the Catalan coast (NW Mediterranean) were ecologically and morphologically analysed and compared. The morphological analysis was performed from body shape of fish species using geometric morphology. Moreover, a canonical correspondence analysis (CCA) was used to analyse the effect of local environmental variables such as habitat, locality and depth on the composition and abundance of assemblages. The results revealed greater differences among assemblages in the clustering performed from morphological data, which is linked to habitat complexity, than those shown by the ecological analysis. Moreover, the CCA analysis indicated that type of substratum and the location significantly influenced the composition and structure of the fish assemblages. These results evidenced that morphology provides different and complementary information than ecological analysis because it allows to predict the ecological and functional habits of species within the community, helping to improve the understanding of the fish assemblages structure.