Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible, yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths, respectively. Using 79 SNP loci, we genotyped nearly 1000 individuals from populations of both species in close proximity to each other and from putative hybrid zones. The species shared all but one SNP polymorphism, and on average, allele frequencies differed by only 0.14. However, the species were clearly differentiated using Structure, and admixed individuals were primarily identified at putative hybrid zones. PopGraph identified a highly integrated network among all populations, but populations of each species and hybrid zones occupied distinct regions in the network. Using either conditional graph distance (cGD) or Fst/(1-Fst), we found significant isolation by distance (IBD) among populations. Within species, IBD was strong, indicating high historic gene flow. IBD extended approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD between the species was very weak and extended only a few km beyond hybrid zones, suggesting little recent gene flow. The extensive sharing of SNP polymorphisms between these species suggests that they are very early in the speciation process while the low signal of IBD suggests that they have largely ceased gene exchange.