Many species adapted to alpine and montane meadow ecosystems are at risk of extinction. The skipper Pyrgus ruralis lagunae Scott is a mountaintop butterfly restricted to San Diego County, CA, a federally listed endangered species, and is in imminent risk of extinction. Historically, P. r. lagunae was found in the Laguna and Palomar mountains. We did not detect the skipper in the Laguna Mountains, and the species has likely been extirpated from this area, which represents half of its historical range and is the type locality. We studied three populations on Palomar Mountain. Skippers primarily occupied areas close to creeks or in adjacent ravines at two nongrazed sites. The third site is grazed by cattle, and skippers were found close to the forest edge. At nongrazed locations, creek areas had higher cover of intermediate-height vegetation, more bare ground, and more flowers compared with unoccupied areas of the same meadow. The vegetation at occupied and unoccupied areas within the grazed meadow were similar. Even so, skippers occupied areas with more bare ground as well as greater species richness of flowering plants. A grazing exclosure was previously installed in an attempt to protect and enhance skipper habitat, but skippers did not use the dense grasslands that developed inside the exclosures. Contrary to the prevailing theory, protection from grazing did not improve skipper habitat. This illustrates how management based on inadequate biological information can hinder well-intentioned conservation efforts.