Isoetes quiririensis is described, illustrated, and compared to similar species. This species can be distinguished from other species in Brazil by a set of characters that include microphylls that are semi-cylindrical in cross section, velum covering more than 3/4 of the sporangium, tuberculate megaspores varying from 477–670 µm in diameter, echinate microspores, and a chromosome number of 2n = 22. We also include a key for species from the Atlantic Rainforest that have tuberculate megaspores, distribution maps, and spore images for all species that are discussed. Isoetes quiriensis is known only from the type locality, where it occurs as an aquatic in small streams at high elevations. We suggest it should be classified as a data deficient species based on the IUCN criteria.