Species delimitation is essential to understanding and categorizing our planet’s biodiversity, particularly amidst rapid changes to environmental conditions and natural landscapes. However, the process of speciation is heterogenous and often complex, and robust characterization of species boundaries has remained a challenge for many taxa. Recent advances in both genomics and ecological modelling have been a boon for research focused on population dynamics, and present new, multidisciplinary opportunities for clarifying species boundaries in taxa that have been difficult to classify otherwise. Here, we present an approach to combining ecological niche models with next-generation sequence data to aid in integrated species delimitation. We apply this approach to the Speyeria atlantis-hesperis (Lepidoptera: Nymphalidae) species complex, which is notorious for its muddled species delimitations, morphological variation and mito-nuclear discordance. Using genomic SNPs, we recovered substantial divergence, not only between S. hesperis and S. atlantis, but also within S. hesperis, which may be attributed to a combination of past introgression with another species, S. zerene, and post-glacial range expansion. We then applied niche modelling to assess ecological divergence and barriers to gene flow among the recovered genomic lineages. Results of these analyses suggest that adaptation to ecological conditions is hindering contemporary gene flow between northern and southern populations of S. hesperis, contributing to and reinforcing their genetic integrity. We suggest that the current species delimitation of S. hesperis should be revised, and demonstrate the utility of an approach to integrated species delimitation that combines ecological and genomic data and reconciles related species concepts.