The pecan weevil, Curculio caryae Horn, is an obligate nut feeder of all hickory (Carya) and a key pest of the pecan, C. illinoinensis Koch. This study investigates population structure of the pecan weevil. Gene flow and genetic variation was estimated for 90 pecan weevil specimens sampled from the entire Carya range. Cladistic and nested clade analyses, as well as an analysis of molecular variance (AMOVA) of mitochondrial DNA cytochrome oxidase I (mtDNA COI) 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, eastern and central localities sampled within C. caryae’s range. 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, C. nasicus approximately 4.3 million years before present (mybp). Lineage divergence between the western and eastern populations occurred during the Pleistocene (approx. 1.1 million years ago), and a more recent divergence occurred between C. caryae populations east and west of the Appalachian mountain range (870,000 yrs. ago). Haplotypes were segregated by region, but further sampling is necessary to test for gene flow among these regions.