The Military Macaw (Ara militaris) is an endangered bird species with disjunct geographic distribution across the Neotropics, consisting of three recognized subspecies: One in Mexico (A. m. mexicanus) and two in South America (A. m. militaris and A. m. bolivianus). However, due to the limited phenotypic differentiation between these allopatric taxa, their taxonomic status has been the subject of debate. In this study, we explored mitochondrial DNA (mtDNA) variability to determine the phylogeographical pattern through phylogenetic and ecological modelling analyses. We also aimed to describe the evolutionary relationships of twelve A. militaris populations. We identified 41 haplotypes in the 300 bp region of the Cytochrome b (Cyt-b) gene of the mtDNA and low nucleotide diversity. The observed phylogeographic structure suggests the existence of two clades: One composed of A. m. militaris and A. m. bolivianus and another consisting solely of A. m. mexicanus. The A. m. mexicanus clade further divides into two recognized subclades: Sierra Madre Oriental and northeastern portion of the Sierra Madre Occidental. Ecological analyses revealed that the niche similarity between these lineages was lower than expected by chance. Additionally, results from low cross-prediction tests indicated that the two lineages have inhabited different environmental spaces since the Late Pleistocene. This divergence may be associated with a steep ecological gradient and contemporary geographical barrier. Based on our results, we suggest that at least the A. m. mexicanus has a divergent evolutionary history; therefore, it should be considered as a different evolutionarily significant and management unit. We recommend that future conservation strategies in Mexico incorporate effective protection measures, including habitat preservation and the reduction of illegal trade, to ensure the preservation of viable populations.
