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Given the interest in the conservation of the Mesoamerican scarlet macaw (Ara macao cyanoptera), the Xcaret Park formed an initial reproductive population about 30 years ago, which has progressively grown to a considerable population in captivity. In this work, we focus on the evaluation of the genetic diversity of the captive population, taking two groups into account: its founding (49) and the current breeding individuals (166). The genetic analysis consisted of genotyping six nuclear microsatellite loci that are characterized by their high variability. Tests for all loci revealed a Hardy–Weinberg equilibrium in four loci of the founders and in no loci of the breeding groups. The results showed that the genetic variation in the Xcaret population was relatively high (founders He = 0.715 SE = 0.074, breeding pairs He = 0.763 SE = 0.050), with an average polymorphism of 7.5 (4–10) alleles per locus in founders and 8.3 (4–14) in breeding pairs. No significant differences in the evaluated genetic diversity indexes were found between both groups. This indicates that the genetic variability in Xcaret has been maintained, probably due to the high number of pairs and the reproductive management strategy. Bayesian analysis revealed five different genetic lineages present in different proportions in the founders and in the breeding pairs, but no population structure was observed between founders and breeding individuals. The analyzed captive individuals showed levels of genetic diversity comparable to reported values from Ara macao wild populations. These data indicate that the captive population has maintained a similar genetic diversity as the metapopulation in the Mayan Forest and is an important resource for reintroduction projects, some of which began more than five years ago and are still underway.