Habitat Conservation Plans (HCPs) are a mechanism used for conserving land and often have an umbrella species associated with them. We conducted occupancy surveys for an umbrella species, the Coastal California Gnatcatcher (Polioptila californica californica), from 2004 to 2009 in San Diego County, California, focusing on preserve lands associated with HCPs. We investigated the effects of habitat quality classification, elevation, distance to coast, and heat load on gnatcatcher occupancy, extinction, and colonization probabilities. Our work focused on these factors throughout the range of this species in San Diego County where, through conservation agreements, a preserve system has been assembled addressing management considerations at a landscape scale. In addition, a large wildfire in 2003 burned 17,044 ha, roughly 1/3 of preserve lands, thus we were able to investigate the recolonization process associated with this event. We found that occupancy increased with habitat quality and over time, but decreased with elevation. Extinction probability was generally constant (∼0.13), but colonization varied greatly, with probabilities being greater in higher quality habitat and at lower elevations. Gnatcatchers were more likely to colonize burned areas adjacent to high and very high quality habitat, sites that should receive priority conservation actions, particularly at lower elevations. Our work suggests that umbrella species, like the California Gnatcatcher, may reflect not just habitat quality, but may also be useful indicators of recovery after an unexpected event such as fire. Although not perfect, the use of multiple umbrella species in HCPs may lead to effective conservation and management of biodiversity hotspots.