Wide-ranging species often span geographic dispersal barriers, providing opportunity for divergence via genetic drift or natural selection. Such conditions can be favorable for speciation, and wide-ranging taxa are frequently subdivided into multiple species by modern molecular studies. However, with wide-ranging species, it is important to explicitly test for isolation-by-distance (IBD), which can produce continuous genetic variation that may be misinterpreted as discrete population structure or even distinct species. Here we examine the Green Frog (Rana clamitans), a wide-ranging species of the Aquarana clade distributed across much of North America. The broader phylogenetic context for R. clamitans within Aquarana is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Florida Bog Frog (Rana okaloosae). Additionally, although phenotypic variation within Rana clamitans previously merited description of two subspecies, patterns of genetic diversity remain unclear. Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana and unambiguously identify R. okaloosae as the sister lineage to R. clamitans. Despite mtDNA introgression, we find little genomic evidence of hybridization between R. okaloosae and R. clamitans. Within R. clamitans there are two well-supported and geographically divided clades, which are identified as distinct species by a multispecies coalescent-based approach. However, the two clades exhibit low genealogical divergence. Population genetic analyses reveal that genetic variation within R. clamitans is best described by a pattern of IBD rather than independently evolving lineages. We conclude that R. clamitans is indeed a single species and the subspecies concept is of limited use. Our analysis demonstrates the importance of understanding continuous genetic variation when delimiting lineages and highlights the power of combining population genetic and phylogenetic perspectives to describe diversity within wide-ranging taxa.