Thirty-three Triatoma sanguisuga (LeConte) adults and nymphs were collected during June and July 2009, at five sites on Cumberland Island and two sites on Sapelo Island, Georgia, to assess genetic diversity within and between sites. All but three specimens were found in a peridomestic habitat. The entire length (699 bp) of the cytochrome oxidase II mitochondrial gene was sequenced for each specimen. Twelve haplotypes were identified, nine from Cumberland Island and three from Sapelo Island. No haplotypes were shared between the two islands, indicating there is limited or no movement of gene flow between the islands. Phylogenetic relationships among the haplotypes were determined using both neighbor-joining and maximum parsimony analyses. The phylogenetic trees from both analyses were similar, with no distinct clades on either tree devoted to haplotypes from a single island. A haplotype network structure was determined using nested clade analysis, which produced two haplotype networks, one containing only specimens found on Cumberland Island. The second network included specimens from both islands, with the ancestral haplotype from Sapelo Island. This pilot study is the first to highlight triatomine populations in the southeastern United States using the cytochrome oxidase II mitochondrial gene, and indicates strong population structuring along the Georgia Coast.