Identification of relationships among geographically distinct populations of migratory species can provide an understanding of breeding and natal philopatry, migration pathways, and population mixing during winter. We used random amplified polymorphic DNA (RAPD) analyses to search for markers specific to difficult‐to‐differentiate shorebird species (e.g. long‐billed dowitcher Limnodromus scolopaceus and short‐billed dowitcher L. griseus) as well as geographically distinct breeding populations of Hudsonian godwits Limosa haemastica, red‐necked phalaropes Phalaropus lobatus, semipalmated plovers Charadrius semipalmatus, dunlin Calidris alpina, pectoral sandpipers C. melanotos, semipalmated sandpipers C. pusilla and western sandpipers C. mauri. Markers clearly differentiated all shorebird species. Estimates of population differentiation varied greatly among species (F_ST= 0.095–0.685) and correlated with interspecific variation in philopatry and geographical separation of breeding populations. We assigned individuals to putative breeding locales with greater certainty in well‐differentiated species than in poorly differentiated species. Our findings indicate specific phylogeographical structure varies among species, which has strong implications for conservation of habitats within migratory corridors. We suggest that RAPDs are useful in identifying geographical populations of migratory species and that molecular markers should be considered for tracking migratory birds throughout the annual cycle.