Peronina Plate, 1893 is a genus of onchidiids that live on the mud in mangrove forests. Peronina can be identified in the field by the lung opening at the margin between the ventral hyponotum and the dorsal notum, and by the distinctive scalloped notum edge. This genus was previously known only from the holotype of the type species, Peronina alta Plate, 1893, from eastern India. Onchidium tenerum Stoliczka, 1869 is moved to Peronina and applies to the same species as Peronina alta. Peronina species are described using an integrative approach (natural history, comparative anatomy and DNA sequences). Mitochondrial COI and 16S sequences and nuclear ITS2 and 28S sequences are used to independently test species boundaries. Mitochondrial sequences yielded three units separated by a large barcode gap, but nuclear sequences yielded two units. Because these two units are congruent with differences in the male copulatory apparatus, they are accepted as species. Explanations for highly divergent COI haplotypes within one species are discussed. Peronina tenera (Stoliczka, 1869) is distributed in the Bay of Bengal and the Strait of Malacca, while P. zulfigari Goulding & Dayrat, sp. nov. is endemic to the Strait of Malacca. The two species differ internally but are cryptic externally.