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Wide application of genetic approaches has enhanced the detection of cryptic diversity, even in historically well-studied organisms. In addition to improving our knowledge of biodiversity, detection of cryptic diversity can have important management implications within imperiled groups, such as the Cuban parrot complex ( Amazona leucocephala). Bahama parrots ( A. l. bahamensis) were once widespread throughout the archipelago, but are now restricted to the two largest islands (Abaco and Inagua). Mitochondrial DNA-based population genetic and phylogenetic analyses revealed the distinctiveness of the Abaco, Inagua and now extirpated Acklins populations, detecting diagnostic character support and reciprocal monophyly indicative of three phylogenetic species. Congruent results were obtained for the Abaco and Inagua populations based on Bayesian clustering analyses of microsatellite genotypic data. Genetic signatures of demographic contraction were identified on Abaco, but not Inagua. These findings were consistent with lower genetics-based estimates of effective population size on Abaco, as well as the disproportionate human impacts reported on the island relative to Inagua. Overall, our results suggest that the taxonomy of the Cuban parrot complex requires revision and that the conservation status of the Abaco phylogenetic species should be immediately elevated to reflect its historical isolation, recent population decline and continued threats to its persistence. [ABSTRACT FROM AUTHOR]