Genetic relationships within the Lygaeus kalmii complex were evaluated using specimens from multiple locations throughout the United States. Genes evaluated included the 18S ribosomal RNA (nuclear) and cytochrome oxidase subunit I (COI, mitochondrial). The 18S rRNA sequences were 100% conserved among all Lygaeus specimens, rendering the gene ineffective for inferring phylogenetic relationships for this project. However, the COI sequences were informative, and a COI-based phylogenetic tree revealed that L. reclivatus Say and both subspecies of L. kalmii (Stål) are closely related, with all falling within the same clade. Twelve different haplotypes of the COI gene were found among the sequences within the L. kalmii angustomarginatus, L. kalmii kalmii, and L. reclivatus clade. Each haplotype differed from other haplotypes by one to six nucleotides (0.13–0.77%), falling within the range of reported intraspecific divergence. Therefore, our data validate the conspecific classification of L. kalmii angustomarginatus and L. kalmii kalmii and suggest that L. reclivatus is not a distinct species. The overlap of haplotypes also suggests possible gene flow among all three groups.