Historically, striped bassMorone saxatiliswere indigenous to many major drainages of the Gulf of Mexico (Gulf). It is believed that almost all natural populations were depleted by the 1950s and 1960s with the exception of fish in the Apalachicola–Chattahoochee–Flint (A–C–F) river system in northwestern Florida, Georgia, and Alabama. Striped bass of Atlantic ancestry were introduced into the A–C–F system during the 1960s and 1970s to enhance population size. We compared DNA fingerprints of striped bass collected from four Atlantic river systems with those offish from the A–C–F system to determine if genetic differences still exist. Moderate levels of polymorphism were observed with two probes, the bacteriophage M-13 genome and mouse sequences related to theDrosophilaPer gene. Striped bass DNA digested with single restriction enzymes and hybridized to these two probes generated single DNA fragments shared by 71 out of 75 A–C–F fish but not seen in any of 51 Atlantic fish. Heritability of DNA fingerprints was demonstrated from hatchery-raised fish of known parents. We believe that descendants of a genetically distinct ancestral Gulf population of striped bass still exist in the A–C–F and that efforts to maintain the genetic integrity of this population are warranted. Screening of potential A–C–F hatchery brood stock may be used to both maintain the genetic integrity of the Gulf strain and maximize its genetic diversity.