Aim To examine the uniqueness and relationship of islands in the San Diegan Province using reef fishes. Location Pacific coast of Baja and Southern California. Methods Quantitative scuba surveys and statistics were used. Between June 2000 and August 2002, the nearshore rocky-reef fishes of eight southern California and Baja California islands were quantitatively surveyed. The islands surveyed were: Santa Cruz, San Nicolas, Santa Barbara, Santa Catalina, San Clemente, North Coronado, San Martin and San Benito. These islands span the latitudinal range of offshore islands within the San Diegan marine province. This regional scale approach provided not only the first quantitative description of rocky-reef fishes at five of these islands, but also allowed comparisons with known biogeographical patterns. Results Here we discuss the distribution and abundance of 84 conspicuous rocky-reef fishes from 35 families. In general, the richness, diversity and composition of fish assemblages at these islands were found to reflect previously described biogeographical processes. The rocky reef fish assemblages of all islands in the survey were found to be significantly distinctive form each other. Phenetic analyses revealed two clusters. San Clemente, Santa Catalina and North Coronado clustered as a warm-water assemblage in the middle of the San Diegan Province. The remaining islands grouped together as a cold-water assemblage, despite the geographically disjunct position of the islands within this cluster. The relatedness of islands was independent of distance. Examination of the most common fish species at all islands revealed that while some conformed to the north-south trending density distributions predicted by previous investigators, the distribution of others could not be explained by latitude or temperature regimes. No single pattern explained the density of fishes at all islands. Both the rock croaker, Pareques sp., and flag cabrilla, Epinephelus labriformis, were observed at San Benito during these surveys, representing northern range extensions and may be indicators of the warming trend observed in this marine province. Main conclusion For nearshore rocky-reef fishes, the islands of the San Diegan marine province are distinct and their interrelatedness is independent of the distance between them.