Mitochondrial Markers <scp>COI</scp> and <scp>16S rRNA</scp> for the Molecular Identification of Parrots and Macaws Recovered From Illegal Trafficking in Three Areas of Colombia

ABSTRACT Illegal wildlife trafficking is a major threat to biodiversity, severely affecting many species, including Psittacidae. In this context, molecular tools such as DNA barcoding provide an effective alternative for taxonomic identification, complementing traditional morphological methods. This study aimed to molecularly characterize parrots ( Amazona spp.) and macaws ( Ara spp.) recovered from illegal trafficking in Colombia using two mitochondrial markers (COI and 16S rRNA). Eighty‐eight DNA samples from whole blood of Psittacidae individuals from three regions (Antioquia, Valle del Cauca, and Cesar) were analyzed. The COI gene provided higher resolution for species identification, generating 65 new sequences and 35 haplotypes (20 Amazona spp. and 15 Ara spp.). Unique haplotypes were found for each species, with clear differentiation in phylogenetic and PCoA analyses. High intraspecific diversity was detected in Amazona amazonica , Ara severus , and Ara ararauna , relevant for future population studies. In contrast, 16S rRNA yielded 77 new sequences clustered into 28 haplotypes (19 Amazona spp. and 9 Ara spp.). However, its low variability limited taxonomic resolution, with poorly defined clusters in haplotype networks and PCoA. Phylogenetic inference supported species‐level grouping under mitochondrial data, except within the yellow‐headed parrot complex. Overall, the COI gene demonstrated greater utility for species identification and genetic characterization in Amazona and Ara species, while the 16S rRNA gene showed limited discriminatory power due to its conserved nature. These findings highlight the value of COI as a reliable molecular tool for wildlife forensic applications and strengthen molecular identification frameworks to combat illegal wildlife trafficking.