<p>Taxonomy of arbuscular mycorrhizal fungi (Glomeromycota) historically has been based mostly on analyses of spore morphology. Molecular evidence has been widely used in phylogeny since the turn of the century and has contributed to the nomenclature of arbuscular mycorrhizal fungi. Considering that some species were described solely from field collected spores which often are degraded, synonymy amongst described species is likely. Type and living cultures of <i>Rhizophagus clarus</i> and <i>Rhizophagus manihotis</i>, and protologue of <i>Glomus zaozhuangianus</i> were analyzed to compare spore wall structure. Sequences of the large subunit (LSU) of the rDNA gene of living isolates of <i>Rhizophagus clarus</i> and <i>Rhizophagus manihotis</i> also were used to test phylogenetic relationships. A comprehensive biogeography of arbuscular mycorrhizal fungi was used to investigate species distribution according to soil and climate factors. Spore wall structure analysis indicates that the three species are morphologically indistinguishable. Spore color, size, and shape all overlap highly among the three species. The spore wall of each is composed of an outer hyaline mucilaginous layer, a rigid hyaline laminated layer conferring a visible “halo” to mature spores, and a third rigid pigmented laminated layer that confers spore color. Phylogenetic analysis shows that living isolates identified as <i>R. manihotis</i> were nested with living isolates of <i>R. clarus</i>, forming a monophyletic clade with 99% bootstrap support. Spores of <i>R. clarus</i> (as amended here) have been recorded in six continents and 31 countries in 10 biogeographical realms. <i>R. clarus</i> was detected most often in soil pH 5.0–6.0, soil P up to 5&#xa0;mg/dm³, and soil organic matter up to 2.5%. Polynomial models indicate that the probability of occurrence of <i>R. clarus</i> is optimized at a temperature of 20^o C and 2,000&#xa0;mm precipitation.</p>