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Heracleum mantegazzianum (giant hogweed) is the largest central European forb, naturalized or invasive in many European countries. The impacts of its colonization of native habitats on soil mesofauna groups are unfortunately obscure. This study assessed the effect of giant hogweed invasion on the communities of plants and soil nematodes in the riparian habitat. We found that invasion by H. mantegazzianum increased soil pH, decreased carbon and nitrogen content, reduced the number and coverage of the native plant species, and influenced nematode communities and their structures. Nematode species number was significantly lower in invaded than uninvaded plots, but nematode species diversity was not affected by invasion throughout the whole study. Total nematode abundance slightly increased under giant hogweed, while total nematode biomass did not differ between the invaded and uninvaded plots. The higher abundance of bacterivores and fungivores but lower number of omnivorous nematodes well represented the negative impact of giant hogweed invasion on soil food webs, supported by low values of all maturity indices or channel index. The hogweed invaded plots contained higher abundance of plant parasitic nematodes, mainly Paratylenchus microdorus. Our results thus indicate that invasion by H. mantegazzianum influences several nematode communities’ parameters while others remain unaffected by invasion.