The morphological, histochemical, and molecular properties of two new species of arbuscular mycorrhizal fungi (AMF; Glomeromycota) have been characterized. The first species is distinguished by spores that are orange to brownish orange, small, and formed only in clusters and mainly by having two laminate layers in a three-layered spore wall, with layer three staining dark in Melzer’s reagent. Despite the morphological similarity to some Septoglomus spp., phylogenetic analyses of sequences of the SSU–ITS–LSU nrDNA region and the RPB1 gene accommodated the fungus in the genus Dominikia, hence it was named Dominika emiratia. Intact spores of the second species, named Rhizoglomus dunense, closely resemble colourless isolates of R. clarum, but their spore wall layer three never becomes coloured with age, as does that in most R. clarum spores, and most importantly, the two fungi are separated by a large molecular distance. Dominikia emiratia was originally extracted from the rhizosphere of three plant species cultivated in two fields in a sandy desert in the Emirate of Abu Dhabi of the United Arab Emirates. Rhizoglomus dunense was found in a trap culture inoculated with the rhizosphere soil and root fragments of Ammophila arenaria, which had colonized sand dunes of the Mediterranean Sea, located near Thessalonica, Greece.