The Black Drum Pogonias cromis is an abundant estuarine‐dependent fish that supports recreational and commercial fisheries. We examined the phylogeography and historical demography of the Black Drum along the Atlantic and Gulf of Mexico coasts of the United States using mitochondrial DNA sequences and nuclear DNA microsatellites. Black Drum exhibited high haplotype diversity and low nucleotide diversity across its range. We observed 249 haplotypes that resolved into two haplogroups: haplogroup 1 was most abundant along the Texas coast, and haplogroup 2 was more abundant in the Atlantic Ocean and the eastern Gulf of Mexico. Analysis of molecular variance, pairwise estimates of genetic differentiation, assessment of isolation by distance, Bayesian clustering, and multivariate ordination indicated that most population structure within Black Drum was associated with a western Gulf of Mexico versus Atlantic–eastern Gulf of Mexico split. However, analysis of molecular variance, haplotype diversity, and measures of genetic differentiation provided evidence of weak population structure on the Texas coast, perhaps due to a of combination of isolation by distance and limited emigration into and dispersal from the upper and lower Laguna Madre on the lower coast. Mismatch distributions, neutrality tests, and Bayesian skyline plots suggest that haplogroup 1 underwent rapid demographic and range expansion approximately 15,000 years ago, whereas the demographic and range expansion of haplogroup 2 was more gradual and began earlier (circa 25,000–30,000 years ago). Our results suggest that Black Drum may benefit from being managed as two stocks: (1) western Gulf of Mexico and (2) Atlantic Ocean plus eastern Gulf of Mexico. Additionally, weak but significant genetic divergence in the Laguna Madre coincides with known life history divergence in this region. Caution should be used regarding the management of Black Drum in Texas as a single demographic unit.