Here we describe the methods and results for biological characterization of the benthos on a previously unexplored area of central California, USA seafloor. We conducted 40 remotely operated vehicle dives from 371 to 1173 m water depth. Seafloor habitats and megafauna (fish and invertebrates) were documented from 46.8 km of seafloor video footage. Our expanded development and analysis of biotopes from quantitative data allowed us to describe detailed biological communities, along with the physical characteristics and habitat associations within the study area. This method provides a framework for potential monitoring, detection of future environmental change (natural and anthropogenic) and comprehensive comparison to other deep water regions. From 185 h of observational video at 25 sites, nearly 120,000 annotations of organisms, habitat characters, biological detritus and anthropogenic debris were recorded and analyzed. We identified a total of 228 taxa, with 173 of them present on linear quantitative transects. Species richness for transects ranged from 0.04 to 0.28 m-2 (8–55 taxa), with densities ranging from 0.07 to 5.20 ind. m−2. Both were highest on hard substrate with greatest surface area. Densities decreased with depth. Within soft substratum zones was a large field of pockmarks, which are seafloor depressions averaging 175 m in diameter and 5 m in depth. Pockmarks have sometimes been associated with seafloor gas seepage, but here we found no biological evidence of chemosynthetic organisms. No significant differences were found in either density nor species richness at pockmark sites vs. non-pockmark sites. Mud draped greenish-black coarse sand occurred only in low oxygen areas, while hummocky, rugose mud supported somewhat different species than flat mud plains. Seventy percent of the transects occurred inside the oxygen minimum zone. We conclude that high rugosity, slope, and the presence of hard substratum were better predictors of species richness and density than oxygen concentration in this specific study. Abundant biological detritus, in the form of dead and dying pelagic pyrosomes and salps, created a large, presumably ephemeral flux of carbon to the seafloor during the study period.