The tropical Andes are a global hotspot of avian diversity that is characterized by dramatic elevational shifts in community composition and a preponderance of recently evolved species. Bird habitats in the Andes span a nearly two-fold range of atmospheric pressure that poses challenges for respiration, thermoregulation, water balance, and powered flight, but the extent to which physiological constraints limit species’ elevational distributions is poorly understood. We report a previously unknown hybrid zone between recently diverged flycatchers (Aves, Tyrannidae) with partially overlapping elevational ranges. The southern Anairetes reguloides has a broad elevational range (0-4200 m), while the northern Anairetes nigrocristatus is restricted to high elevations (>2200 m). We found hybrids in central Peru at elevations between ~3100-3800 m, with A. nigrocristatus above this elevation and A. reguloides below. We analyzed variation in hematology, heart mass, morphometrics, plumage, and one mitochondrial and three nuclear loci across an elevational transect that encompasses the hybrid zone. Phenotypic traits and genetic markers all showed steep clines across the hybrid zone. Hemoglobin concentration, hematocrit, mean cellular hemoglobin concentration, and relative heart mass each increased at altitude more strongly in A. reguloides than in A. nigrocristatus. These findings suggest that A. nigrocristatus is more resistant than A. reguloides to high-altitude hypoxic respiratory stress. Considering that the ancestor of the genus is suggested to have been restricted to high elevations, A. reguloides may be secondarily adapted to low-altitude. We conclude that differential respiratory specialization on atmospheric pressure combined with competitive exclusion maintains replacement along an elevational contour, despite interbreeding.