In pine wilt disease, xylem dysfunction occurs in relation to nematode migration and proliferation in host tissue, but the detection accuracy of pinewood nematode (PWN), Bursaphelenchus xylophilus, in pine stem tissue remains unclear. This study describes the use of cryo-scanning electron microscopy (cryo-SEM) and fluorescein-conjugated wheat germ agglutinin (F-WGA) staining to detect PWN. After PWN invasion, the frequency of surface fluorescence in PWN increased in pine stems from the day of inoculation to 3 weeks after inoculation. However, the fluorescence frequency decreased significantly during the advanced disease stage after 5 weeks. Thus, detecting PWN based on fluorescent staining of the nematode body surface coat protein can be misleading when used to examine the correlation between the development of disease symptoms and the nematode population. In contrast, all cut body segments were fluorescent, and their fluorescent components were common in pine-stem cross sections, regardless of the timing after inoculation. In addition, PWN were observed under cryo-SEM only in empty resin canals and this distribution was confirmed by F-WGA staining of PWN cut in a cross section. Thus, PWN detection based on fluorescent staining of surface coat proteins by F-WGA was not reliable in longitudinal sections of pine stems because of changes in nematode stainability during disease progression. To detect PWN in infected plants, we concluded that a combination of both methods is most effective.