In order to characterize the biodiversity of the benthic invertebrate by-catch associated with the shrimp fishery at Farol de São Thomé harbour, northern Rio de Janeiro State, Brazil, in 2004, 11 monthly trawls were conducted using bottom trawl nets between 22°00’S and 22°20’S and from 3 to 5 nm from the shoreline. The analyzed data for each taxon and/or species include frequency of occurrence, numeric frequency, biomass, Index of Relative Importance, and abundance. In total, 27 benthic invertebrate species were recorded, including Porifera, Cnidaria, Mollusca, Annelida, Crustacea, Echinodermata, and Bryozoa. The most representative group was Crustacea, both in number of specimens (Petrochirus diogenes, Hepatus pudibundus, Callinectes ornatus) and in biomass (P. diogenes, H. pudibundus). In terms of the frequency of occurrence in the samples, 11 species (40.7%) were constant, 6 species (22.2%) were accessories, and 10 species (37.0%) were by-catch.