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Burnaby size-adjusted principal component analysis of 14 morphological characters revealed significant differences among sites for the third principle component, which explained 6% of the total variation. Analyses of electrophoretic loci showed significant allele frequency heterogeneity among sites for one of seven polymorphic loci. The magnitude of the morphological and genetic differences between the Marquesas Keys sample and both of the Atlantic coast samples was generally greater than between the geographically more distant Cape Canaveral and Cape Lookout samples, although overall levels of variation among sites were small. Estimates of gene flow suggest that relatively frequent migration, sufficient for panmixia in the absence of historical divergence, may occur between populations. Our results suggest that oceanographic processes play a critical role in the transport of <i>A. gibbus</i> larvae between populations. 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