We describe a large and distinctive new treefrog species with blue webbing from the west coast of the Masoala peninsula in northeastern Madagascar. Boophis masoala sp. n. is morphologically similar to the other species of the Boophis albilabris group but can be distinguished from them easily by several chromatic characters of the eyes. Despite its similar morphology, it is genetically highly differentiated (10.5–13.3% pairwise p-distance in a segment of the 16S rRNA gene) from all other species in the B. albilabris group including the morphologically most similar Boophis praedictus. Both species share the blue webbing between toes and are distributed on the Masoala peninsula, but so far were not found in close sympatry. Although we recorded the new species only from the unprotected areas near the coast, we are confident that it also occurs within the adjacent Masoala National Park. We discuss the importance of eye colouration as a predictor of specific distinctness in the genus Boophis and that of webbing colouration as taxonomic characters of large treefrogs. Based on a micro-CT scan we provide a comprehensive description of the osteology of the new species, which is the first for any Boophis species, and furthermore describe its distress call which consists of three distinct sections corresponding to (1) the starting phase with closed mouth, (2) the opening of the mouth and (3) the final section with an open mouth.