The new stonefly species, Neoperla mindoroensis sp. nov. (Perlidae), from Mindoro island is described. The new species is assigned to the N. recta species complex of the N. montivaga group on account of its obvious T7 and T8 with pointed processes and the presence of basolateral lobes in the everted aedeagal sac. The male adult is distinguishable by its aedeagus with a slightly raised mediodorsal lobe, fully covered with fine spinules, while the female adult has comparably small eggs (240 × 220 μm) with a punctate, chorionic surface with punctae arranged in polygonal FCIs­. The life stages and sexes were assigned using COI mtDNA barcodes (2.2% maximum intraspecific genetic distance), which were compared with available barcodes of congeners, which had interspecific genetic distances varying by at least 23.5%. Biogeographic aspects, ecological habitat requirements, and suitability as potential bioindicator of the species are also briefly discussed.