Here, we describe a new ornamented arbuscular mycorrhizal (AM) fungus, Racocetra crispa sp. nov. isolated from maize fields from the central region of Minas Gerais State, Brazil. For the first time, a Glomeromycotina species is described using a long continuous nuclear rDNA sequence fragment, which encompasses the nearly complete 18S SSU sequence gene until the 3′ end of the D2 region of the 28S LSU (~ 3100 bp), which allows for comparison with sequences obtained from regions used for fungal metagenomic studies, species description, and AMfungi DNA-barcode. The new species forms dark brown to black spores, approx. 340–510 μm on in diam., on sporogenous cells. The spores have unique Bcloud/flower^ projections on the spore surface, two walls, and differentiate a multiple-lobed germ shield with up to 8–12 germ tube initiations. The analysis of the intra- and interspecific DNA-barcode sequence variation within the Racocetra showed that the intragenomic polymorphism among the clones of R. crispa (0–2 %) is within the lower range for the genus. The V3–V4 region of the SSU nrDNA has no resolution to discriminate Racocetra at species level, but from this fragment, we found homology between R. crispa and environmental sequences from two metagenomics studies, one carried out in Brazil at the fungus type location and the other in New Zealand. The integration between AM fungal sequences from reference strains and those obtained from environmental sequences in Glomeromycotina is still a problematic issue, mainly due to the reduced number of AM fungal species characterized based on DNA sequences.