We studied the genetic variability of Platypelis species (Anura: Microhylidae) with red flash marks from Madagascar based on mitochondrial (16S rRNA) and nuclear (RAG1) genes. Our molecular phylogenetic results suggest that the red colour evolved independently in the Platypelis barbouri complex and P. milloti and confirm the validity of a long-known but still undescribed new species from eastern Madagascar. Platypelis ranjomena sp. nov. is distinctly coloured with dark red to purple patches at the base of the forelimbs, in the inguinal region, and on the ventral parts of the hind limbs. It differs from most other arboreal cophylines by this red colour and from its sister species P. barbouri by smooth dorsal skin texture, iris colour, bioacoustics (much longer note duration in advertisement calls), and genetics (strong differences in mitochondrial and nuclear markers). The new species is widespread at low elevations along the east coast from Marojejy in the north to Manombo in the south. However, genetic evidence indicates substantial intraspecific variability among populations, suggesting that the taxonomy of P. ranjomena and the other species in this complex is still incompletely resolved. An individual of P. barbouri from Mahasoa shared a nuclear allele with P. ranjomena, and its call was to some degree intermediate between these species, suggesting a possible case of hybridization in an area that we hypothesize could be a contact zone between the two species. Individuals from Madagascar's northeast hitherto assigned to P. barbouri represent a lineage that is sister to the clade of P. barbouri + P. ranjomena. It is herein identified as a new candidate species (Platypelis sp. Ca11), which occurs in syntopy with P. ranjomena.