The genus Lygus is widely distributed in North America and Eurasia. The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), is one of the most serious pest species within this genus. This pest has over 300 known host plants. We employed various molecular markers to investigate both inter- and intra-specific genetic diversity of North American Lygus spp. The mitochondrial (mt) cox1 barcode region and a 768-bp region overlapping cox1 and cox2 were sequenced. A nearly complete mt genome (14454 bp) sequence was obtained from L. lineolaris. Neighbor-Joining (NJ) trees indicate that most L. lineolaris individuals belong to two closely related clades, thus indicating a sympatric distribution and the potential existence of cryptic species within L. lineolaris. The intraspecific mtDNA variation within regional populations and between widely dispersed populations of L. lineolaris was found to be similar, which suggests a lack of geographically based population structure for this species. The genetic diversity of other North American Lygus species (L. hesperus, L. keltoni, L. borealis, L. elisus, L. vanduzeei, and L. plagiatus) has also been investigated. Multi-species phylogenetic analysis shows that L. plagiatus, L. elisus, and L. borealis predominantly have their own clades. Two species, L. hesperus and L. keltoni, are not differentiated by mtDNA. The apparent absence of monophyly in these species pairs could indicate recent separation or within species variation of physical characters.