Striped bass (Marone saxatilis) from the Apalachicola River, Florida; Chattahoochee-Flint River, Georgia; Ogeechee River, Georgia; Savannah River, Georgia; Santee-Cooper River, South Carolina; Tallapoosa River, Alabama; and Chesapeake Bay, Maryland, were examined for polymorphism in their mitochondrial DNA (mtDNA) genotype. The Xba I site loss that is supposed to identify individuals with matemallineage from Gulf Coast stocks was found in some fish from the Apalachicola and Chattahoochee-Flint rivers, as well as one individual from the Ogeechee River. Additionally, a unique Bgl I site gain was found in these same populations. Several rare genotypes found in the Apalachicola-Chattahoochee-Flint system were also rare genotypes in Chesapeake Bay. Several unique genotypes of low frequency were found in the Ogeechee River. Fish from the Santee-Cooper River were fixed for a unique Dra I genotype. The only other population exhibiting this Dra I genotype was found in the Tallapoosa River, confirming stocking history of Santee-Cooper fish into this system. Composite genotypes were distinctive for most of the fish sampled in the Apalachicola River and all individuals from the Santee-Cooper River.