Pedicularis growing at Mt. Halla of Jeju Island is known as an endemic species of P. hallaisanensis Hurusawa. On the other hand, the plant is morphologically similar to P. amoena, P. spicata, and P. verticillata in gross morphology, so the taxonomic treatment of the taxon remains controversial. To clarify the taxonomic position of the plants, we examined external morphological characters and nuclear ribosomal DNA ITS sequences for P. hallaisanensis and its related species. The plants of Mt. Halla are clearly different from P. amoena and P. verticillata in the morphology of calyx lobes, the length of galea and lower lip, density of glandular hairs on plants, presences of the radical leaves after anthesis and molecular data. However, P. hallaisanensis is not clearly separated from P. spicata distributed in N. E. Asia on external morphological characters and DNA sequences of internal transcribed spacers. In this study, the morphological and molecular data suggested that P. hallaisanensis should be merged into the former species.