Stationary underwater video surveys were conducted on rocky habitats near Loreto and coral habitat at Cabo Pulmo in the Gulf of California to obtain non-cryptic reef fish distribution and abundance data. Measurements of habitat variables were recorded to investigate the influence of habitat on fish distribution and abundance. Differences in fish assemblages were greatest between Loreto and Cabo Pulmo with differences also detected among the three islands sampled at Loreto. At Isla Carmen, fishes were associated with habitat variables of relief, rugosity, boulder diversity, and percent cover but not habitat type, indicating an influence of habitat morphology on reef fish assemblage structure. Results were similar to other studies conducted in the central Gulf of California indicating stability of reef fish assemblages in the region, although factors other than habitat likely play a greater role in structuring reef fish assemblages there.