Isoetes naipiana (Isoetaceae), a new species from southern Brazil, is described, illustrated and compared to similar species. So far it is known only from the original locality in the open grasslands of the upper highlands in the NE region of the State of Rio Grande do Sul (Brazil). It is characterized by megaspores with an irregular reticulum on the surface, presenting deposition of thin parallel silica strands; laevigate microspores; and arcuate microphylls with shortly alate bases, forming a compact rosette around the erect bilobate corm.