The Gulf of California has a high variety of ecosystems that allow different services and the fishery resources play a prominent role in its ecology, evolution and economics. Fish coastal species have been previously reported for most coastal areas, especially those species that are subject to fishing, however, little is known on the species from deep sea zones, due to sampling difficulties. We studied the deep sea fishes collected with trawl nets during three research surveys in the Gulf of California, Mexico in 2004-2005. We provide a systematic checklist and some notes on biogeographical aspects. For this, 74 fishing hauls were done, and a total of 9 898 fishes were captured, belonging to two classes, 15 orders, 35 families, 53 genera and 70 species. The best represented families in number of species were: Paralichthyidae (eight), Serranidae (six), and Scorpaenidae and Triglidae with five species each one. The typical families from deep waters were: Ophidiidae, Moridae, Lophiidae, Scorpaenidae, Triglidae, Paralichthydae, Pleuronectidae and Cynoglossidae. Size range varied from 13cm for the Splinose searobin (Bellator xenisma) to 234cm in the Pacific Cutlassfish (Trichiurus nitens). The biogeographical affinity showed that species with affinity to the East Tropical Pacific (ETP) dominated, followed by species from San Diego-Panamic, San Diego-Panamic-Peruvian-Chilean and Oregonian-Cortes provinces, respectively. A biogeographic overlap was found in the fauna, which reflects the Gulf of California's geographical position, with distribution limits of species from temperate, tropical and warm-temperature transition affinities, divisions that characterize the Gulf of California. Taxonomic status of fish with a focus on composition, location, characterization and zoogeography are fundamental to any subject of biodiversity and fisheries management actions.