San Diego County is attempting a proactive conservation planning effort to protect endangered, threatened, and other sensitive species at the landscape level. This plan is being completed under the State of California's Natural Community Conservation Planning (NCCP) program. When completed, a series of individual Habitat Conservation Plans (HCPs) will provide a system of interconnected reserves designed and managed for biological conservation. The NCCP program has been the center of significant controversy since its inception, yet it has been touted as a national model. This paper explores some of the key lessons that have been learned during implementation of the largest and most complex HCP approved under the NCCP—the Multiple Species Conservation Program—since its adoption five years ago. The exploration of the successes and impediments faced by the Multiple Species Conservation Program should help others developing habitat conservation programs in their future efforts to protect endangered species and their habitats.