Wide-ranging species are often polytypic, span geographic dispersal barriers, and experience opportunities 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. Although Rana clamitans is phenotypically variable enough to previously merit description of two subspecies, patterns of genetic diversity remain unclear. Additionally, the broader phylogenetic context for R. clamitans is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Bog Frog (Rana okaloosae). Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana and unambiguously identify R. okaloosae as the sister lineage to R. clamitans. Within R. clamitans we find two well-supported and geographically divided clades which are identified as distinct species by a widely used genetic species delimitation method, BPP. However, the two clades exhibit low genealogical divergence and 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 emphasizes how existing approaches can erroneously split species characterized by continuous genetic variation and highlights the power of combining population genetic and phylogenetic perspectives to better understand diversity within wide-ranging taxa.