De facto marine protected areas (DFMPAs) are regions of the ocean where human activity is restricted for reasons other than conservation. Although DFMPAs are widespread globally, their potential role in the protection of marine habitats, species, and ecosystems has not been well studied. In 2012 and 2013, we conducted remotely operated vehicle (ROV) surveys of marine communities at a military DFMPA closed to all civilian access since 2010 and an adjacent fished reference site at San Clemente Island, the southernmost of California’s Channel Islands. We used data extracted from ROV imagery to compare density and biomass of focal species, as well as biodiversity and community composition, between the two sites. Generalized linear modeling indicated that both density and biomass of California sheephead (Semicossyphus pulcher) were significantly higher inside the DFMPA. Biomass of ocean whitefish (Caulolatilus princeps) was also significantly higher inside the DFMPA. However, species richness and Shannon-Weaver diversity were not significantly higher inside the DFMPA, and overall fish community composition did not differ significantly between sites. Demonstrable differences between the DFMPA and fished site for two highly sought-after species hint at early potential benefits of protection, though the lack of differences in the broader community suggests that a longer trajectory of recovery may be required for other species. A more comprehensive understanding of the potential conservation benefits of DFMPAs is important in the context of marine spatial planning and global marine conservation objectives.