The San Joaquin coachwhip, Masticophis flagellum ruddocki, (SJCW) is a large diurnal snake endemic to the San Joaquin Desert of California. The SJCW is a subspecies within the continent-spanning coachwhip species group, and was diagnosed on the basis of unique color traits. High resolution genetic analysis of SJCW has not previously been attempted. In order to better inform conservation of this endemic species and to learn more about its historical and present-day relationships with other subspecies, we conducted extensive tissue sampling and genetic analysis of the species in the San Joaquin and Salinas Valleys, and across the wider desert southwest, primarily through salvage of roadkilled specimens. We report on population structure both within the subspecies and across the species' range.