AbstractThe scarlet macaw, Ara macao, is a neotropical parrot that contains two described subspecies with broadly discrete geographical distributions. One subspecies, A. m. macao, is found from South America north into southwestern Costa Rica, while the second subspecies, A. m. cyanoptera, is found from eastern Costa Rica north into central Mexico. Our previous research using mitochondrial data to examine phylogeographical divergence across the collective range of these two subspecies concluded that they represent distinct evolutionary entities, with minimal contemporary hybridization between them. Here we further examine phylogenetic relationships and patterns of genetic variation between these two subspecies using a dataset of genetic markers derived from their nuclear genomes. Our analyses show clear nuclear divergence between A. m. macao and A. m. cyanoptera in Central America. Collectively however, samples from this region appear genetically more similar to one another than they do to the examined South American (Brazilian) A. m. macao sample. This observation contradicts our previous assessments based on mitochondrial DNA analyses that A. m. macao in Central and South America represent a single phylogeographical group that is evolutionarily distinct from Central American A. m. cyanoptera. Nonetheless, in agreement with our previous findings, ongoing genetic exchange between the two subspecies appears limited. Rather, our analyses indicate that incomplete lineage sorting is the best supported explanation for cytonuclear discordance within these parrots. High-altitude regions in Central America may act as a reproductive barrier, limiting contemporary hybridization between A. m. macao and A. m. cyanoptera. The phylogeographic complexities of scarlet macaw taxa in this region highlight the need for additional evolutionary examinations of these populations.