Bursaphelenchus doui was isolated from a dead Japanese red pine, Pinus densiflora, in Shizuoka, and from the tracheal system of a species of longhorn beetle, Monochamus subfasciatus, collected at Tama Forest Science Garden of Forestry and Forest Products Research Institute, Tokyo, Japan. The Japanese populations of B. doui were compared with the original description of material obtained from coniferous packaging materials imported from Taiwan and Korea to continental China. Additional characters from the Japanese population include a constricted female mucron with a step-like appearance and several morphometric values. The molecular profiles of the Japanese B. doui populations were determined by DNA sequencing and ITS-RFLP profiles and were compared with those of the Taiwanese and Chinese populations of B. doui and other species in the genus. The phylogenetic analysis of the small subunit and large subunit ribosomal DNA indicated that B. doui is clearly included in the xylophilus-group of the genus Bursaphelenchus and may be close to B. conicaudatus and B. luxuriosae. The potential risk of B. doui for pine species is considered to be relatively low because B. doui did not display any pathogenicity to Japanese black pine in an inoculation test.