Reproductive isolation is central to the speciation process, and cases where the strength of reproductive isolation varies geographically can inform our understanding of speciation mechanisms. Although generally treated as separate species, Black-capped chickadees (Poecile atricapillus) and Carolina chickadees (P. carolinensis) hybridize and undergo genetic introgression in many areas where they come into contact across the eastern United States and in the northern Appalachian Mountains. The Great Smoky Mountains harbor the last large breeding population of atricapillus in the southern Appalachians, isolated from the species’ main range by nearly 200 km. This population is believed to be reproductively isolated from local carolinensis due to an unusual, behaviorally mediated elevational range gap, which forms during the breeding season and may function as an incipient reproductive isolating mechanism. We examined the effectiveness of this putative isolating mechanism by looking for genetic introgression from carolinensis in Great Smoky Mountain atricapillus. We characterized this population and parental controls genetically using hundreds of amplified fragment length polymorphism (AFLP) loci as well as mitochondrial DNA (mtDNA) sequence data from cytochrome-b. Great Smoky Mountain atricapillus have experienced nuclear genetic introgression from carolinensis, but at much lower levels than other populations near the hybrid zone to the north. No mitochondrial introgression was detected, in contrast to northern contact areas. Thus, the seasonal elevational range gap appears to have been effective in reducing gene flow between these closely related taxa.