The Lilac-crowned Amazon (Amazona finschi) is an endemic parrot from western Mexico with a historical distribution in the Pacific Slope from southern Sonora and southwestern Chihuahua to Oaxaca. However, a particularly worrying decline in the extension of its distribution range has been reported in the central and southern regions. Overall, the species is listed in CITES the IUCN Red List of Threatened Species, and the official Mexican standard NOM-059 as endangered. In this study, we aimed to obtain molecular information to support the planning of conservation strategies for A. finschi. For this purpose, we analyzed the genetic diversity and genealogical relationships between two groups of individuals from northern (Sinaloa) and central (Michoacan) portions of the species’ range based on mitochondrial DNA markers. In general agreement with the endangered status of the species, we found low genetic diversity values. However, at the regional level, the northern group showed high genetic diversity and the central group showed a lack of genetic diversity. Furthermore, in agreement with the proposal that A. finschi is monotypic, genealogical relationships revealed a haplotype distributed in the center and the north, although haplotypes exclusive to the north were also found. We suggest a differentiated management of northern and central populations to preserve evolutionary potential.