Bobcats (Lynx rufus) are valuable indicators of connectivity in the highly fragmented landscape of coastal southern California, yet their population sizes and densities are largely unknown. Using noninvasive scat sampling in a capture–recapture framework, we estimated population sizes for 2 similar areas of natural habitat with differing levels of isolation by human development in Santa Monica Mountains National Recreation Area, California. We used scat transects with geographic information system land-use layers and home-range sizes of bobcats to estimate effective sampling area and population densities. Estimates of population size in the study area connected to a much larger habitat area (26–31 individuals) were similar to estimates for the area that was completely surrounded by development (25–28 individuals). Bobcat densities for the 2 study areas also were similar (ranging from 0.25 to 0.42 bobcat/km²) and likely represent recent population declines because of notoedric mange likely interacting with toxicants. These methods proved effective despite particularly low densities of bobcats and may be especially useful when study areas are geographically isolated, reducing the uncertainty in size of the sampling area.