We describe a new species from the cophyline microhylid genus Rhombophryne, a group of fossorial and terrestrial frogs endemic to Madagascar. Found during herpetofaunal surveys of moist montane forest in the remote north of Ranomafana National Park, Rhombophryne nilevina sp. n. exemplifies two difficulties that hinder taxonomic progress in Malagasy cophyline frogs: micro-endemicity and highly secretive habits. Known from only two adult male specimens, this new species is nonetheless easily distinguishable from all other known Rhombophryne using morphological data, and osteological data collected here via X-ray Micro-Computed Tomography, or “micro-CT”. This species is now the largest known Rhombophryne, and the only one known from Ranomafana National Park, which will make it the southern-most member of the genus pending a forthcoming taxonomic revision involving Plethodontohyla and Rhombophryne. Pairwise distances of the mitochondrial 16s rRNA marker show a minimum genetic distance of 4.9% from other nominal Rhombophryne. We also describe recordings of an advertisement call, emitted from a burrow by the holotype. Rhombophryne nilevina sp. n. is not known to be found syntopically with other Rhombophryne, nor to be present elsewhere in Ranomafana National Park, but it probably does co-occur with a few ecologically similar Plethodontohyla species. Although the type locality is within a protected area, we suggest an IUCN listing of Data Deficient for R. nilevina sp. n., as its area of occupancy is largely undetermined within the park.