We examined genetic population structure of five putative subspecies of Song Sparrows (Melospiza melodia) in the San Francisco Bay region (M. m. samuelis, M. m. maxillaris, M. m. pusillula, M. m. gouldii, and M. m. heermanni) at nine microsatellite loci to assist the development of Song Sparrow conservation and management strategies. We sampled nine populations from five putative subspecies and found low estimates of differentiation between populations within subspecies and between. Despite low estimates of divergence, genetic structure at the subspecies level was indicated by the larger amount of variance accounted for by subspecies than populations. We propose that a management unit encompassing the range of M. m. pusillula be given priority for conservation on the basis of the extent of genetic divergence shown by Cavalli-Sforza and Edward's chord distance, and the topology of an unweighted pair group cluster analysis supported by 100% of bootstrap replicates across loci. Although M. m. samuelis and M. m. maxillaris appear undifferentiated from M. m. heermanni, it remains possible that adaptive differences between those types were not identified with neutral loci.