Allocation of evolutionary divergence into species level versus subspecies ranks is critical for conservation and management. Urocitellus brunneus (Idaho ground squirrel; formerly Spermophilus brunneus) is currently apportioned into 2 subspecies, U. b. brunneus and U. b. endemicus, but recent studies have suggested elevation to distinct species based on differences in pelage, bacular morphology, genetic data, timing of life-history cycle, and behavior. Following recent movements toward integrated taxonomy, we use the cohesion species concept to test whether both genetic and ecological data support species-level classification of U. b. brunneus and U. b. endemicus. Eight microsatellite loci and mitochondrial DNA (mtDNA) sequence data were generated for 339 individuals from 14 localities for U. b. brunneus and 312 individuals from 11 localities for U. b. endemicus. The null hypothesis of genetic interchangeability was tested with 2 independent data sets. First, we estimated an mtDNA gene tree from control region and cytochrome-b sequences via parsimony, maximum-likelihood, and Bayesian analyses. We then tested for evidence of recent migration using Bayesian clustering and coalescence analyses of microsatellite data. The 2nd null hypothesis, that of ecological exchangeability, was tested using an ecological niche-model analysis and a review of the literature based on morphology, habitat characteristics, and behavior. Although divergence of mtDNA sequences between the subspecies was modest (<1%), there are no haplotypes shared between the 2 taxa. There is strong support for monophyly of mtDNA haplotyes of U. b. endemicus (posterior probability  =  0.94), with those from U. b. brunneus forming a basal grade. No evidence of recent gene flow was detected; the Bayesian clustering algorithms of mutlilocus genotype data indicated separate ancestry for both U. b. brunneus and U. b. endemicus. The ecological-niche model showed a nonoverlapping niche for each taxon, allowing for the possibility of differential adaptation. We reject both null hypotheses based on the data, which supports elevation of U. b. brunneus and U. b. endemicus as distinct species.