We systematically surveyed 94 of the 122 nearshore rocky reefs in the California south coast study region (SCSR). This synoptic baseline survey was conducted at 75 individual sites in 2011 and 88 sites in 2012. In addition, we incorporate two similar ‘historical’ data sets from 59 sites in 2004 and 79 sites in 2008. From 2011-2012, we surveyed all accessible nearshore rocky reefs found in the SCSR MPAs and determined the appropriateness of references areas for each. This baseline provides, for the first time, a taxonomically exhaustive biogeographic assessment of the nearshore subtidal reefs in the SCSR, improving significantly on our knowledge of the region and incorporating newly established and existing MPAs. Results confirm previously described patterns for subtidal fishes, reflect the physical oceanographic complexities of the Southern California Bight and add new knowledge to biogeographic patterns of algae and invertebrates. The SCSR is characterized by strong environmental gradients, a major defining feature of the SCSR compared to the other California MLPA Study Regions that have relatively more spatially consistent physical environments. These differences are reflected biologically in a high degree of kelp forest community structure across the region. We identified 17 geographically cohesive community clusters, each with distinct fish, invertebrate, and algal assemblages (Figure ES.1). Although kelp forest communities in the SCSR are highly variable, the structure can be related to the sea surface temperature patterns caused by the confluence of the California Current, the Southern California Counter Current and localized upwelling. Benthic habitat structure also varies within the region; the geology and structure of island reefs are functionally different from mainland reefs. Mainland reefs generally are less steep, can be found significantly offshore of the coastline, and have a greater influence of sedimentation moving through the system. With few exceptions, island reefs are generally abrupt, high relief structures, tightly fit to the coastline with less influence of the nearby soft bottom habitat. Ideally, long-term monitoring of MPAs should be distributed across the distinct areas as each is likely to respond differently.