Population genetic analyses that depend on the assumption of neutrality for allozyme markers are used widely. Restriction fragment length polymorphisms in nuclear DNA of the American oyster evidence a pronounced population subdivision concordant with mitochondrial DNA. This finding contrasts with a geographic uniformity in allozyme frequencies previously thought to reflect high gene flow mediated by the pelagic gametes and larvae. The discordance likely is due to selection on protein electrophoretic characters that balances allozyme frequencies in the face of severe constraints to gene flow. These results raise a cautionary note for studies that rely on assumptions of neutrality for allozyme markers.