Vaccinium parvifolium Sm. (Ericaceae) is an important understory shrub in conifer forests in western North America. Populations putatively classified as V. parvifolium in northern California display alternate berry morphology, consistent with a possible phenotypic diversification or cryptic speciation. Identification of cryptic species or subspecies would influence management guidelines given the limited range of some morphological variants. In order to inform management guidelines, two Vaccinium species were characterized via molecular genetic analyses. Plants of typical V. parvifolium morphology from the coastal areas of northwest California, western Oregon and Washington, atypical plants from Shasta County and the central Sierra Nevada, and one population of V. deliciosum Piper, a congener, were assessed at five nuclear microsatellite loci. Analyses of differentiation, admixture, and phylogenetic relationships indicated that populations displaying atypical morphology were more similar to V. deliciosum than to the typical V. parvifolium. Although additional data are required to determine whether these differences warrant taxonomic treatment within Vaccinium, management plans should consider three distinct gene pools among these populations.