The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), is a highly polyphagous insect pest. It is the most widely distributed Lygus species in North America, and it is the most prevalent member of the genus Lygus in the eastern half of the continent. We sampled multiple populations of L. lineolaris from three disparate regions of North America, and used parts of the mitochondrial genes cytochrome oxidase 1 and cytochrome oxidase 2 as markers to assess intraspecific diversity of this species. Results indicated that there is an association between genetic population structure and geography. Neighbor-joining, maximum parsimony, Bayesian inference analysis, and maximum likelihood trees suggested that most L. lineolaris individuals belong to two closely related clades showing sympatric distribution. Mitochondrial DNA haplotypes common to widely dispersed populations were observed. Morphological identities of five L. lineolaris samples that formed an outlier clade indicated incongruence between morphological identity and genetic data. Individuals from the two major clades and one disparate clade did not exhibit recognizable morphological differences. No strong host plant associations were observed among clades, thus, genetic structuring in this species appears to mostly be geographically based. This study represents the first attempt to survey cytochrome oxidase 1 and cytochrome oxidase 2 variation within L. lineolaris and to use those genes to construct a molecular phylogeny for this species.