One of the main concerns of shrimp fisheries is the associated impact on ecosystem biodiversity, particularly on fish assemblages that are poorly characterized yet likely very relevant to the health of the ecosystem. The continental shelf along the eastern coast of the mouth of the Gulf of California is a region of high biodiversity that harbors highly productive fisheries. This study aimed to analyze the changes in the soft bottom fish assemblages caught as bycatch in the shrimp fishery located in this region. Sampling was conducted with commercial trawls at 16 fixed stations during the 2006–2007 shrimp-fishing season. A total of 103 fish species from 80 genera and 47 families were collected. The ecological and taxonomic diversity as well as the composition and abundance of the fish community caught as bycatch in the shrimp trawl fishery were found to be significantly different in the autumn and winter. Ordination and similarity analyses also revealed differing patterns. Species abundance was strongly associated with sea bottom temperature, depth and latitude. The effects of these abiotic variables on the observed diversity patterns and the possible influences of the fishery are discussed.