Hybridization and introgression between two closely related but taxonomically distinct Arctic lousewort species — the circumpolar Pedicularis hirsuta L. (predominantly eastern Arctic in Canada) and the amphi-Beringian, western Canadian Pedicularis langsdorffii Fisch. ex Steven subsp. arctica (R. Br.) Pennell ex Hultén — is documented here for the first time; only the second confirmed case of introgression in this widespread genus. Multivariate and univariate analysis of morphological characters successfully delineate the two species as morphologically similar but distinct taxa. Analysis of nrDNA ITS sequences likewise differentiate the two taxa in all sampled instances. Analysis of cpDNA atpI–atpH sequences also separate these taxa, except in 12 individuals of P. langsdorffii subsp. arctica, which possess the same haplotype as P. hirsuta. Where these two species overlap in range in the Canadian High Arctic, chloroplast transfer from P. hirsuta to P. langsdorffii subsp. arctica is detected, and morphologically intermediate hybids have been identified, indicating hybridization and subsequent backcrossing. Here we discuss the relationships between these two species, and provide a key that is useful for differentiating them.