The Nipomo Mesa lupine (Fabaceae; Lupinus nipomensis Eastw.) is a critically endangered annual species endemic to San Luis Obispo County, California. The species has an area of occurrence of less than 6 km2, and yearly estimates of individuals have ranged from ca. 150 to 1,600—an exceedingly small number for an annual species. Nipomo Mesa lupine faces several threats to its survival, including invasive species, herbivory by small mammals and invertebrates, habitat loss and fragmentation, and increasingly variable rainfall and temperature. Because the threats to survival are coupled with a highly restricted distribution and low numbers of individuals, the Nipomo Mesa lupine is at risk of extinction. Ongoing conservation strategies have sought to establish ex-situ populations on adjacent protected lands, to bulk seed for long-term storage, to better characterize the habitat requirements and threats, and to develop a comprehensive conservation and management plan which will inform recovery efforts. Taxonomically, there has been some doubt about the species status of L. nipomensis. In the 1959 California Flora, Munz placed the species in synonymy under Lupinus concinnus, and a note in the current treatment in the Jepson Manual suggests that the species circumscription is somewhat unclear due to introgression with L. concinnus. These lingering taxonomic uncertainties have hindered conservation efforts. Here, we provide morphological and molecular phylogenetic evidence to demonstrate that L. nipomensis is a well circumscribed species evolving as a separate lineage from other closely related annual species, especially L. concinnus.