Filenchus fungivorus n. sp., isolated from autumn bellflower (Gentiana scrabra Bunge) in Japan and maintained on a fungus culture, is described based on LM, SEM and molecular data. The new species is characterised by combination of the following features: two lateral lines, short body (284-331 μm), short stylet (7.0-8.7 μm), amphid aperture associated with characteristic depression, short ovary, undifferentiated spermatheca, post-vulval sac shorter than corresponding body diam. and short (59-80 μm) non-filiform, almost straight tail and absence of males. According to a principal component analysis, a small tail/vulva-anus (1.3-1.8) and V′ ratio have the highest morphometrical power to separate F. fungivorus n. sp. from the remaining analysed Filenchus spp. (with the exception of F. misellus). Molecular analyses based on SSU rDNA placed F. fungivorus n. sp. within a clade that contained Filenchus sp. (heathland, Belgium), F. (Ottolenchus) discrepans, Malenchus andrassyi and F. misellus. However, the position of this clade could not be resolved within the Tylenchomorpha. Although the phylogenetic analyses, confirmed by Shimodaira-Hasegawa tests, significantly rejected the monophyly of Filenchus (P < 0.001), F. fungivorus n. sp. is placed within Filenchus in anticipation of a review of the Tylenchidae.