The Atlantic horseshoe crab (Limulus polyphemus), a long-lived marine arthropod, is a prime example of a common-pool resource across its native range from Maine to the Yucatan Peninsula, being both a vital ecological food source and a valuable commercial commodity. Genetic differentiation and diversity of horseshoe crabs have been assessed on a regional level, but no fine-scale examinations of these measures had been conducted in South Carolina. A suite of 12 microsatellite loci was used to evaluate the population structure and genetic diversity of spawning adult horseshoe crabs (n = 740) collected from seven sites along the coast of South Carolina from the Georgia/South Carolina border to Bulls Bay. No significant genetic differentiation was detected among the sites, indicating that some degree of gene flow is occurring along the South Carolina coast and that spawning adult horseshoe crabs in South Carolina form a single, unified stock. The horseshoe crab stock in South Carolina contains moderately high levels of genetic diversity (H_o = 0.775_,H_e = 0.778) and fairly low levels of inbreeding (F_IS = 0.005). The effective population size is on the order of several thousand individuals and within the values recommended to maintain evolutionary potential. The information generated here will be useful for management purposes to aid in the regulation and preservation of the horseshoe crab stock and fishery in South Carolina.