The Greenlandic and west-central Siberian breeding populations of Sanderlings Calidris alba are separated by ca. 2000 km during the breeding season, but mix in Europe to some extent during migration. However, the number of Siberian Sanderlings that spend the non-breeding season along the East Atlantic Flyway (extending from western Europe to South Africa), if any, is unknown. Although both populations are considered part of the nominate subspecies C. a. alba based on morphology, population structure in Sanderlings has yet to be described with molecular methods. We examined genetic differentiation at the mtDNA control region (CR) and seven microsatellite loci between Greenland- and Siberia-breeding Sanderlings in order to: (1) develop a diagnostic tool for assessing the breeding origin of Sanderlings along the East Atlantic Flyway, and (2) provide a comparison with the co-distributed and ecologically similar Red Knot, in which CR differentiation of geographically analogous populations (C. canutus islandica and C. c. canutus) has indicated isolation of lineages near the time of the last glacial maximum. By contrast, we found only weak differentiation between the Sanderling breeding populations at the CR, and no differentiation at microsatellite loci. These results suggest that the assignment of breeding origin of Sanderlings on Afro-European flyways will not be possible with simple and inexpensive genetic methods, and imply that Sanderlings and Red Knots have very different post-glacial phylogeographic histories.