In North America, the sunflower (Helianthus annuus L.) has been serving humans for over 5,000 years, and sunflower has had a long association with its native pests, the red sunflower seed weevil (Smicronyx fulvus LeConte) and grey sunflower seed weevil (Smicronyx sordidus LeConte). The seed weevils can cause severe damage where commercial sunflowers are grown. We are using partial nucleotide sequences of the nuclear 18S rRNA gene (18S rDNA), the mitochondrial 16S rRNA gene (16S rDNA) and the 12S rRNA gene (12S rDNA) to investigate genetic differences among 46 sunflower seed weevil populations collected in a north-south pattern on both sides of the Rocky Mountains. We have isolated and analyzed sequences of the three gene fragments from 29 populations. The analyses were performed under several algorithms in PAUP* 4.0 10b. We demonstrated clear and diagnostic separation of the two morphologically similar species. We found differences in nuclear and mitochondrial DNA among populations. We will determine whether such differences, as well as differences in microsatellites, can be related to recent geologic history of the region; and whether the data indicate that the mountains served as reproductive barriers. The data may also provide clues as to the place of origin of sunflower seed weevils in North America.