The structure of genetic variation in flowering plants has rarely been studied at a wide range of spatial scales. In the montane herb Ipomopsis aggregata, allozymic variation has previously been examined at the two extremes of geographic and microspatial scales. Here we assessed morphometric and allozymic variation at intermediate scales by sampling from three localities approximately 25 km apart. Within each locality we sampled three populations 2.5 km apart, and within each population we sampled three subpopulations (250 m apart), each of 50 plants. Hierarchical F-statistics based on ten polymorphic allozyme loci revealed significant variation across individuals, subpopulations, populations, and localities. As spatial distance between sampling points increased, genetic distance increased and indirect estimates of gene flow, based on Fst, decreased. Gene flow at the subpopulation and population levels can result from extraterritorial flights made by hummingbird pollinators, whereas gene flow at the locality level is likely to represent movements during hummingbird migration. The scale of differentiation was different for allozymes and floral morphology. For allozymes, variance components decreased monotonically with spatial scale, whereas for morphological characters the variance component among localities was higher than the population variance component. Three hypotheses are proposed to account for the high among-locality variance in floral morphology (1) environmental effects on morphology, (2) genetic differences resulting from locality dependent selection, and (3) introgression from l. tenuituba.