The marine waters surrounding La Jolla, California have a diverse array of habitats and include several marine protected areas (MPAs). We compiled a list of the fish species occurring in the vicinity based on records of specimens archived in the Marine Vertebrate Collection (MVC) of the Scripps Institution of Oceanography (SIO). Collection of fishes from La Jolla in the MVC started in 1905, but greatly accelerated in 1944 when Carl L. Hubbs moved to SIO. By 1964, 90% of the 265 species recorded from the area had been collected and archived in the MVC. The fishes of La Jolla are dominated by species whose center of distribution is north of Point Conception (111 species), or between there and Punta Eugenia (96), with fewer species with southern distributions (57), and one exotic species. Reflecting the diversity of habitats in the area, soft-substrate species number 135, pelagic species 63, canyon-dwelling species 123 (including 35 rockfish species of the genus Sebastes), and hard-bottom species 140. We quantified the abundance of the latter group between 2002 and 2005 by counting visible fishes in transects along the rocky coastline of La Jolla, both within and adjacent to one of the region's MPAs. In 500 transects, we counted over 90,000 fishes representing 51 species. The fish communities inside and outside of the MPA were similar and, typical of southern California kelp forests, numerically dominated by Blacksmith, Chromis punctipinnis (Pomacentridae), and Señorita, Oxyjulis californica (Labridae). Natural history collections such as the MVC are important resources for conservation biology for determining the faunal composition of MPAs and surrounding habitats, and documenting both the disappearance and invasion of species.