<p><i>Rhamdia quelen</i> is a species complex of considerable importance for artisanal fisheries and aquaculture, making it a conservation priority in Uruguay. Formerly classified under the family Pimelodidae, <i>Rhamdia</i> has since been reclassified into the family Heptapteridae. Previous studies have identified multiple mitochondrial lineages of <i>R. quelen</i> based on one or a few mitochondrial genes. More recently, population genomic studies have revealed the existence of two genomic lineages (North and South) that show evidence of mitochondrial introgression. However, the close correspondence between the distribution of genomic and mitochondrial lineages may reflect a shared evolutionary history. Our objective was to characterize the mitochondrial genome of <i>R. quelen</i> and assess its diversity among mitochondrial lineages from the Uruguay basins. Additionally, we examined the evolutionary history of Heptapteridae species within the superfamily Pimelodoidea. Phylogenetic analyses positioned <i>R. quelen</i> (Heptapteridae) as a sister group to the clade comprising Pimelodidae and Pseudopimelodidae. Evidence of purifying selection was observed across all protein-coding genes in <i>R. quelen</i>. Our analyses confirmed the existence of three mitochondrial lineages, with genetic distances ranging from 3 to 6%. Although previous studies have reported mitochondrial introgression, our findings highlight the complex evolutionary history of <i>R. quelen</i>, suggesting the presence of additional genomic lineages beyond those previously identified.</p>