The Red Crossbill (Loxia curvirostra complex) endemic to the South Hills and Albion Mountains in southern Idaho has coevolved in a predator-prey arms race with the lodgepole pine (Pinus contorta latifolia). The resulting divergent selection has favored a sedentary, locally adapted crossbill population whose size and vocalizations differ from those of co-occurring Red Crossbills of other call types. It has also led to high levels of reproductive isolation between the “South Hills crossbill” and nomadic taxa with different vocalizations that move in and out of the area yearly. Genetic analyses of amplified fragment length polymorphisms (AFLP) indicate that about 5% of the loci in the South Hills Crossbill have diverged in spite of the potentially homogenizing influence of gene flow. Given these differences in genetics, morphology, and behavior, and the high level of reproductive isolation in sympatry with other call types (99% of South Hills Crossbills pair assortatively), we recommend that this crossbill be recognized as a distinct species.