In this study we investigated the communities of soil nematodes in the forest habitats invaded and uninvaded by Fallopia japonica (Houtt.) Ronse Decr., in Tatra National Park, Slovakia. We found that invasion by F. japonica altered nematode communities and their structures. Total nematode abundance, species number and nematode biomass were significantly lower in invaded than uninvaded plots, but species diversity remained unaffected throughout the study. The overall abundance of all nematode trophic groups well represented the negative impact of F. japonica invasion on soil food webs, supported by low values of all maturity indices, a structural index and the Jaccard index of faunal similarity. A weighted faunal analysis similarly characterized the food webs of invaded plots as poorly developed or highly disturbed, with bacterial decomposition and a low C/N ratio. Our findings thus suggest that dense plots of knotweed simplify the structural complexity of the soil environment by reducing the richness of plant species, which may have contributed to the negative changes in the structures of the nematode communities.