Microorganisms that cause human diseases can contaminate fishes in aquatic environments as well as during their capture, handling, and transport. The purpose of this study was to isolate Vibrio parahaemolyticus and Salmonella enterica from fishes captured in the Lagoa dos Patos estuary that were eviscerated and cleaned for trade. Thirteen fish landing were analyzed and 65 entire fishes and 65 cleaned fishes were studied to determine the presence of V. parahaemolyticus and S. enterica. Bacterial isolates were compared using rep-PCR. V. parahaemolyticus was isolated from one entire Micropogonias furnieri and two entire Mugil platanus, as well as from three eviscerated M. platanus. S. enterica was isolated from two eviscerated Paralichthys orbignyanus. Identical rep-PCR bands from V. parahaemolyticus were observed in entire and eviscerated fishes from the same discharge, suggesting processing failures that neither eliminated the microorganism from the raw material nor prevented cross-contamination. S. enterica was not isolated from entire fishes, presumably because contamination occurred due to hygiene and sanitary failures. Our results showed that M. furnieri and M. platanus captured in the Lagoa dos Patos estuary may host V. parahaemolyticus and that this microorganism, as with S. enterica, may also persist even after the fish is cleaned. This is the first record of the isolation of V. parahaemolyticus from M. furnieri.