A new arbuscular mycorrhizal (AM) fungus, Microkamienskia peruviana, was detected in bait cultures for arbuscular mycorrhizal fungi established with rhizospheric soil substrates of the inka nut (Plukenetia volubilis). The field soil derived from three agricultural plantations in the Amazonia lowlands of the province Lamas, San Martin State, in Peru. The fungus was subsequently propagated in single species cultures on Sorghum sp., Brachiaria sp., Medicago sativa and P. volubilis as host plants. The new species differentiates hyaline spores regularly in spore clusters, up to 500–800 × 400–600 μm. The spores are 16–31(–36) × 13–29(–35) μm in diam, formed on cylindrical or slightly funnel-shaped hyphae, without a septum at or close to the spore base. Phylogenetically, the new fungus belongs to a new genus, named Microkamienskia, which has as type species M. perpusilla comb. nov. and to which also M. divaricata comb. nov. belongs. Both are transferred from Kamienskia to Microkamienskia in the present study. The new fungus can be identified by the ballooning semi-persistent to evanescent outer spore wall layer in PVLG-based mountants that is not known for the other species of these two genera, nor for any other glomeromycotan species of similar small spore sizes. Kamienskia and Microkamienskia species can be distinguished by their position in the phylogenetic tree and by hyaline spores, open pores at the spore bases and in the subtending hyphae, and by their spore sizes that are for Microkamienskia among the smallest spore sizes so far detected for AM fungi (15–35 μm).