In a three part study, we analyzed: (1) population-level response of the coachwhip snake, (Masticophis flagellum) and striped racer (M. lateralis) to fragmentation of scrub habitats in coastal southern California using site occupancy models and presence/apparent absence data; (2) space-use behavior of coachwhip snakes and racers in fragmented and continuous habitats of coastal southern California using data from radio-telemetry; and (3) phylogeography and population genetic variation throughout the range of both species with emphasis on coachwhip populations in southern California using mitochondrial DNA sequence and RFLP data. Part 1 revealed disproportionate loss of coachwhip populations from fragmented areas. Unlike the racer, the coachwhip tended to be absent from sites embedded in isolated landscapes, even at large spatial scales. The two species showed large differences in rates of local extinction and probability of detection, with coachwhip populations exhibiting variable rates of detection and greater likelihood of local extinction. Habitat composition influenced site occupancy. Coachwhip snakes preferred sites with open sage scrub and grassland. Racers preferred scrub dominated sites. In Part 2 coachwhip snakes exhibited great plasticity in spacing and movement patterns between sites, showing large differences in movement response to changes in local conditions and amount of available space. In sympatry, coachwhip snakes and racers showed large differences in home range size, rate of travel, and movement distance, with coachwhip snakes ranging more widely than racers. Differences in habitat use fit well with occupancy patterns. Coachwhip snakes utilized both scrub and grassland, and racers utilized largely only scrub. In Part 3 phylogenetic analyses recovered significant structure in both species, with seven well-supported and geographically coherent clades recovered from coachwhip populations sampled throughout the range of the species. High density sampling within southern California recovered four cryptic coachwhip lineages in contact and organized geographically by bioregion. Collectively, results suggest the greater vulnerability of the coachwhip to land-use change is related to differences in habitat use, movement, and rates of population turnover. Unless the few remaining large, contiguous landscapes of grassland and open scrubland are incorporated into regional conservation planning, long-term persistence of coachwhip lineages is unlikely in the future landscape of California.