The loggerhead sea turtle Caretta caretta is a globally threatened species. The southeasternUnited States of America (USA) nesting assemblage is one of the two primary loggerheadrookeries in the world and the largest in the Atlantic. Determining the stock structurewithin this nesting aggregation is important for defining management units and providingbaseline data for mixed stock analyses of foraging aggregations and stranded turtles. I conductedmolecular analyses utilizing mitochondrial DNA (mtDNA) sequence and newly developedmicrosatellite primers on samples collected from nine sample sites from North Carolinato the Florida panhandle to characterize the population structure of rookeries comprising thesoutheastern USA nesting assemblage. Pairwise comparisons of mtDNA haplotype frequenciesamong eight sample sites utilizing genetic distance-based and frequency-based modelssuggested significant structure among most sites tested in Florida. Pairwise F-statistics andR-statistics revealed no significant nuclear allele frequency differences among any of the ninesample sites. This pattern of complex population structure may be attributable to migrationmediatedgene flow among nesting beaches that are discrete by virtue of female nest sitefidelity. However, pairwise tests of genotypic frequency divergence did suggest shallow butsignificant differences between Georgia and Florida sites and South Carolina and Floridasites, consistent with the segregation of northern subpopulation and Florida loggerheads onforaging grounds supported by carapace epibiont and tagging studies. Analysis of molecularvariance (AMOVA) and pairwise comparisons suggested that the currently designated southFlorida management unit may be comprised of multiple management units. More extensivegeographical sampling is required to make more robust inferences about the integrity andboundaries of management units.