A new fungal species was detected in bait cultures of arbuscular mycorrhizal (AM) fungi grown in and on roots of Zea mais and Oryza sativa as host plants. These plants were initially inoculated with rhizospheric soil substrate derived from a cocoa (Theobroma cacao) plantation in the Amazonia lowlands of the province of Lamas, San Martin State, in Peru. The fungus differentiated globose to subglobose spores in the bait culture, singly or in small, relatively loose clusters with up to 30 spores, terminally on pigmented subtending hyphae and have open pores, and thus resemble spores of the genus Rhizoglomus. The spores are yellow-white to whitish yellow or creamy yellow, (63–)70–97(–101) × (63–)70–89(–97) in diameter and have three wall layers. In Melzer’s reagent, the outer layer stains greyish to pinkish, while the middle and inner layer stain dark purple to almost black. Phylogenetically, the new fungus clusters within Rhizoglomus in a separate clade, closest to R. silesianum, R. natalense, R. vesiculiferum, R. irregulare and R. venetianum. It is here described under the epithet Rhizoglomus cacao. An identification key for all species in the genus Rhizoglomus is updated in this study.