Differences in oceanographic conditions over short distances can dramatically affect the distribution of marine organisms over small spatial scales. In southern California, oceanographic conditions vary widely from east to west as the offshore region is impacted by cool, southern flowing California Current water, while the inshore is typically warmer and more productive. We investigated how patterns of distribution and abundance of larval, genetically identified rockfishes related to environmental conditions off southern California, the world’s center of rockfish Sebastes spp. species diversity. The rockfish assemblage was dominated by small and short-lived species not typically targeted by recreational or commercial fishing (i.e. shortbelly S. jordani and squarespot S. hopkinsi rockfishes), but also contained moderate abundances of a few larger, targeted species (bank S. rufus and bocaccio S. paucispinis rockfishes). Spawning locations of many species were affected by environmental variability, as abundances of young (0 to 2 d old), targeted larvae were mainly found offshore in the cool, low primary production waters that also were relatively shallow and contained hard substrate. In contrast, untargeted species were more widespread and correlated positively only with hard substrate. Hotspots of species richness and targeted species were high within a large managed region, the Cowcod Conservation Area, indicating that it is effectively protecting important rockfish spawning habitat. This research highlights the need to account for environmental variation in habitat and assemblage structure when conducting marine spatial planning.