Few studies have analyzed the genetics of Andean bear (Tremarctos ornatus) populations through the use of the hypervariable D-Loop mitochondrial region. This approach can be useful for the assessment of genetic diversity and ancestral lineages. In the present study we evaluate the genetic status of an Andean bear population in northern Ecuador using D-loop mtDNA sequence polymorphisms. For this purpose, DNA from individuals sampled in the Metropolitan District of Quito was used to amplify and sequence a fragment of the hypervariable D-loop region. Our results show remarkably low levels of genetic diversity, based on haplotype (H) and nucleotide (π) diversity indices, and low pairwise genetic distances between haplotypes. Phylogenetic analyses suggest that these haplotypes are clustered into a single monophyletic group. These diversity indices are among the lowest reported for any bear population, suggesting a need to establish or revise the current conservation strategies in the region.