The pecan weevil, Curculio caryae (Horn) (Coleoptera: Curculionidae), is an obligate nut feeder of all hickory (Carya spp.) and a key pest of the pecan, Carya illinoinensis Koch. This study investigates population genetic structure of the pecan weevil. Gene flow and genetic variation was estimated for 90 pecan weevil specimens sampled within the range Carya occurring in the United States. Cladistic and nested clade analyses, as well as an analysis of molecular variance of mitochondrial DNA cytochrome oxidase I were performed. Six-hundred and forty equally parsimonious trees of 31 haplotypes demonstrated high genetic diversity across all pecan weevil samples, and significant regional subdivision. Three clades recovered in the parsimony and nested clade analyses were strongly associated with western, central, and eastern localities sampled within the range of C. caryae. The current distribution of C. caryae and population structure were explained by past glaciation events. The data indicate C. caryae diverged from its sister species, Curculio nasicus (Say), ≈4.3 million years before present (mybp). Lineage divergence between the western and eastern populations occurred during the Pleistocene (≈1.1 million mybp), and a more recent divergence occurred between C. caryae populations east and west of the Appalachian mountain range (870,000 yr ago). Haplotypes were segregated by region, but further sampling is necessary to test for gene flow among these regions.