Wells, R. J. D., James H. Cowan Jr, and William F. Patterson III. 2008. Habitat use and the effect of shrimp trawling on fish and invertebrate communities over the northern Gulf of Mexico continental shelf. ICES Journal of Marine Science, 65: 16101619. The goals of this study were to characterize habitat-specific fish and invertebrate community structure over sand, shell-rubble, and natural reef substrata, and to assess the effects of trawling on the sand and shell-rubble habitats and their associated communities during quarterly trawl surveys over a 2-year period. Fish and invertebrate communities differed significantly among habitat types [analysis of similarities (ANOSIM); Global R = 0.436, p < 0.001), and with respect to trawling exposure (ANOSIM; Global R = 0.128, p < 0.001). Habitat characteristics were quantified from video transects sampled with a remotely operated vehicle, and included percentage coverage of tubeworms, bryozoans, anemones, corals, and algae, significantly affecting fish community structure. Diversity indices differed among habitats, with the highest Shannon diversity (H) and Pielou's evenness (J) over shell-rubble, specifically non-trawled shell-rubble. In addition, higher values of H and J were found over trawled sand relative to non-trawled sand habitats. Length frequency distributions of several abundant fish species showed truncated size distributions over trawled and non-trawled habitats and were both habitat- and species-specific. The study describes habitat-specific differences in community structure, highlighting the differences between trawled and non-trawled areas on the northern Gulf of Mexico continental shelf.