Population segregation catalyzes genetic differentiation and can lead to speciation. Population genetic structure is also critically important for population management, especially in species characterized by small, isolated populations. Sandhill Crane (Antigone canadensis) populations of the Pacific flyway are made up of breeding populations nesting west of the Rocky Mountains, and isolated by intermediate mountain ranges. Current management policy in British Columbia treats all Sandhill Cranes as a single population, whereas in the western United States subpopulations are subject to population specific management. Here, we analyze microsatellite markers, mitochondrial DNA sequences, and mitochondrial haplogroups, derived from 203 individual Sandhill Cranes to elucidate population genetic structure of cranes migrating along the Pacific Flyway to summer breeding habitat on the North and Central Coast of BC and southeast Alaska. STRUCTURE, AMOVA, FST, DAPC, and phylogenetic analyses reveal geographically separated crane populations along the west coast of North America show substantial genetic differentiation in the Pacific Flyway. These findings are consistent with behavioural and ecological evidence - divergent diets, flyways and breeding habitats. We conclude the unique characteristics of coastal Sandhill Crane populations deserve special management consideration relative to interior and southwestern Alaskan crane populations. The conservation of Pacific Flyway Sandhill Cranes depends on safeguarding the genetic diversity and adaptations within and between populations to protect these cranes from current and future climate scenarios, and by protecting the breeding, staging and wintering habitats of each population.