Coastal habitats are essential for ecological processes and provide important ecosystem services. The Galapagos archipelago has a wide diversity of ichthyofauna which preservation guarantees the functioning of the marine ecosystem. In this study, we used ecological and taxonomic indices as well as multivariate analysis to identify spatiotemporal changes in fish community structure in coastal habitats of San Cristóbal Island in the southeastern Galapagos archipelago. We analyzed how the patterns of variability were related to the abiotic conditions (substrate, sea temperature and depth) of each habitat. Nine sites affected by anthropogenic influence (fishing and tourism) representing different habitats/substrates were sampled. Underwater surveys were conducted during the warm and cold seasons in 2010 and 2011 at transects that varied in depth according to site. Artificial habitat, followed by coral and rocky habitats, had the highest diversity, evenness, and taxonomic distinctness, while mangrove habitats had the lowest values. This was related to the habitat complexity and possible anthropogenic influences. While the diversity patterns were more strongly related to the type of substrate, followed by the combination of substrate and depth, and the sea temperature had less influence. These findings were related to the ecological traits of the fish communities and their mobility between habitats. Temporal changes in fish community diversity and composition were not detected at all sites, suggesting that these species have high fidelity to their habitats and a high environmental tolerance that allows them to persist in their habitats despite strong changes in sea temperature on the Galapagos archipelago.