The virulence of Bursaphelenchus xylophilus, the pine wood nematode, varies greatly among different populations. Two inbred strains, called P3 and P9, were recently established via repeated full-sib mating. They exhibited remarkable differences in pathogenicity-related traits. Although their propagation did not differ when cultured on fungal lawns, P9 reproduced better in host seedlings and exhibited higher virulence. In the present study, we obtained fundamental information about P3 and P9 in terms of tolerance to oxidative stress and examined this tolerance and the cuticular ultrastructure. P9 survived better under hydrogen peroxide (H2O2)-stressed conditions than did P3. In addition, P9 had a thicker cuticle than P3. Although further studies are needed, these results suggest that the difference in tolerance in P3 and P9 was due not only to physiological features, such as H2O2-degrading ability, but also to physical factors (cuticle thickness).