A new arbuscular mycorrhizal fungus, Septoglomus nigrum, was found in several agricultural field sites in France, Germany and Switzerland, especially in extensively to intensively managed natural meadows and pastures and in extensively managed cropping systems. The fungus was propagated in trap pots and single species cultures on Lolium perenne, Trifolium pratense, Plantago lanceolata and Hieracium pilosella. It differentiates black spores with triple-layered walls, 95–175× 90–170 μm in diameter, formed singly in soils or rarely in roots. Phylogenetically, it forms a distinct clade close to S. altomontanum and S. africanum, which can morphologically be distinguished from spores of S. nigrum by the characteristics of the spore wall and by the color, size and shape of the subtending hyphae. An identification key is provided that differentiates all species so far described in Septoglomus.