Song Sparrows (Melospiza melodia) provide one of North America’s best examples of geographic variation in phenotype, with approximately 26 described subspecies recognized. However, researchers have found inconsistent signals when making comparisons between subspecies and genetic markers. We examined seven microsatellite loci from 576 Song Sparrows of 23 western North American populations representing 13 recognized subspecies. We assessed the level of concordance between microsatellite genotypes and subspecies. We found that in some, but not all, instances neutral genetic structure corresponded to recognized phenotypic structure. However, some populations not currently recognized as subspecies were found to be genetically differentiated from all other populations that are considered to be the same subspecies. We suggest that a combination of phenotypic characters, behavioral traits, and multiple loci be used when assessing geographic variation in birds, and that sampling should be conducted in more than one location within broadly distributed subspecies.