The diatom flora of tropical freshwater environments of South America is unique when compared to temperate areas of the continent such as Austral and Antarctic zones, where the species composition tends to present many cosmopolitan elements. The present work describes a new diatom species from the Chapada Diamantina (BA, Brazil), a semi-arid region of Northeastern Brazil, belonging to the recently described monospecific genus Perinotia Metzeltin & Lange-Bertalot. This work also provides additional information oil valve structure observed under electron and light microscopy for the generitype. Perinotia diamantina differs from the type species, P. jankae Metzeltin & Lange-Bertalot, by presenting greater valve width and smaller length/width ratio. Irregularly distributed puncta around the terminal raphe endings also differ between P. diamantina from P. jankae. Ecological information for both species is given.