Genetic variation and population structure of Synanthedon pictipes (LPTB) from 3 locations in Arkansas was examined using DNA sequences of a 603 bp region of the mitochondrial cytochrome oxidase I gene (COI), tRNA-leu and cytochrome oxidase II gene (COII). From 114 LPTB collected from 3 populations, a total of 53 nucleotide positions were polymorphic, with 12 haplotypes. The greatest amount of haplotype diversity was seen in Fayetteville where borer management is not maintained. High levels of gene flow were observed between the Clarksville, Springdale and Fayetteville populations suggesting the LPTB has a broad dispersal range. TCS examination of genealogical relationships and PAUP* phylogenetic analysis of the 12 haplotypes gives genetic support for 3 subspecies.