The ecologically and economically important arbuscular mycorrhizal (AM) fungi, crucial in the ecology and physiology of land plants, and the endocytobiotic fungus, Geosiphon pyriformis, are phylogenetically analysed by their small subunit (SSU) rRNA gene sequences. They can, from molecular, morphological and ecological characteristics, unequivocally be separated from all other major fungal groups in a monophyletic clade. Consequently they are removed from the polyphyletic Zygomycota, and placed into a new monophyletic phylum, the Glomeromycota.

The recognition of this monophyletic group, which probably diverged from the same common ancestor as the Ascomycota and Basidiomycota, gives these fungi their proper status, and provides a basis for a new and natural systematics of these fascinating, yet largely hidden organisms, with three new orders (Archaeosporales, Paraglomerales, Diversisporales) described herein. Additionally, several clades resolve at family level; their formal description is in progress.