Species of arbuscular mycorrhizal fungi (Glomales, Zygomycetes) are discrete entities recognized by distribution of phenetically well-defined characters and related by common descent. A model of macroevolution is proposed in which (i) mutualism arose between an asexually-reproducing terrestrial plant and zygomycete fungus, (ii) speciation of arbuscular fungi occurred while mutualism evolved and spread among radiating plant lineages, (iii) species persisted from time of origin to present day relatively unchanged in spore phenotypes and with zero rate extinction, and (iv) evolutionary changes in the fungi following speciation involved modification of mycorrhizal phenotypes to maximize co-adaptation of clones and host species. Species are considered historical entities, with clonal populations as the fundamental units of contemporary evolutionary change. Experimental results can be extrapolated to the level of species or supraspecific taxa only with an adequate sampling of dissimilar clonal populations.