Geographical variation in microsatellite allele frequencies and morphology were compared for five subspecies of Melospiza melodia (song sparrow; M. m. samuelis, M. m. maxillaris, M. m. pusillula, M. m. gouldii, and M. m. heermanni) in 14 populations in the San Francisco Bay region to (a) assess divergence based on these estimates and (b) test the hypothesis that drift is responsible for morphological and genetic divergence. Morphological differentiation between subspecies was high despite low differentiation at microsatellite loci, indicating high gene flow and large effective population sizes. Low concordance of morphological and genetic estimates of divergence suggests that selection or phenotypic plasticity in morphology has caused morphological differentiation among the subspecies.