The population genetic structure of 251 bonnethead sharks, Sphyrna tiburo, from estuarine and nearshore ocean waters of the Western North Atlantic Ocean (WNA), was assessed using sequences of the mitochondrial DNA-control region. Highly significant genetic differences were observed among bonnetheads from 3 WNA regions; Atlantic coast of Florida, Gulf coast of Florida, and southwestern Gulf of Mexico (analysis of molecular variance, ΦCT = 0.137; P=0.001). Within the Gulf coast of Florida region, small but significant genetic differences were observed between bonnetheads from neighboring estuaries. These overall patterns were consistent with known latitudinal and inshore-offshore movements that occur seasonally for this species within US waters, and with the residency patterns and high site fidelity to feeding/nursery grounds reported in estuaries along the Atlantic coast of Florida and South Carolina. Historical demography also supported the occurrence of past population expansions occurring during Pleistocene glacial-interglacial cycles that caused drastic reductions in bonnethead population size, as a consequence of the eustatic processes that affected the Florida peninsula. This is the first population genetics study for bonnetheads to report genetic divergence among core abundance areas in US and Mexican waters of the WNA. These results, coupled with recent advances in knowledge regarding regional differences in life-history parameters of this species, are critical for defining management units to guide future management strategies for bonnetheads within US waters and across international boundaries into Mexico.

Sharks are a priority for conservation because numerous species, including small‐sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and preventing population declines. Limited dispersal is an important factor promoting population divergence for several coastal shark species. The genetic variation in 14 microsatellite loci and 21,006 single nucleotide polymorphisms genotyped using restriction‐site‐associated DNA sequencing was analysed to assess the genetic structure of the bonnethead shark, Sphyrna tiburo, in the western North Atlantic. Genetic differences were identified among three well‐defined regions: the western Florida coast, the south‐eastern US Atlantic coast, and the southern Gulf of Mexico. Results support previous studies based on mitochondrial DNA sequences in defining differences among these regions and suggest limitations of bonnethead sharks in routinely performing long‐distance migrations. The limited connectivity among regions explains the pattern of genetic divergence but also reported divergence at the species/subspecies level. These genetically discrete bonnethead populations have independent evolutionary histories that may include local adaptations to specific areas. Bonnethead sharks are currently managed as two stocks in the USA owing to recent genetic, tagging, and life history studies; however, no stock assessments or management plans exist for Mexico. These results not only serve to reinforce US management strategies and provide critical data about the extent of gene flow and sex dispersal among populations, but also begin the process of effective management in the waters of Mexico to ensure the long‐term productivity and resilience of this species. With an absence of gene flow between populations from US waters and the southern Gulf of Mexico, there is a need for management plans based upon independent biological and population dynamics data since limited or no opportunities for populations to interchange individuals may occur to re‐establish population viability.