Black drum Pogonias cromis and P. courbina are the only two valid species at present within the genus. These species support extensive commercial and recreational fisheries along the Western Atlantic coasts. Recent studies qualify the species P. courbina as vulnerable. We used two mitochondrial markers, partial sequences of cytochrome oxidase I and cytochrome b genes, to study genetic variation and demographic history of P. courbina from the Río de la Plata and the adjoining Southwestern Atlantic Ocean. Additionally, for the first time, we used both markers to estimate the divergence time of the species in the genus Pogonias. Regarding the study of the species P. courbina, the results obtained indicate relatively moderate to low levels of genetic variation. Besides, we found evidence that P. courbina has experienced a recent population expansion during the Pleistocene in the Río de la Plata and adjacent waters of the Southwestern Atlantic Ocean. Our analysis has shown that P. cromis and P. courbina diverged 1,154,800 years ago. The present work suggests a certain vulnerability to overexploitation and therefore conservation measures should be implemented to avoid population decline of P. courbina in the Río de la Plata.