Mantellid frogs present an extensive adaptive radiation endemic to Madagascar and Comoros, being the subfamily Mantellinae the most morphologically and ecologically diverse. The Mantellinae present key innovative evolutionary traits linked to their unique reproductive behavior, including the presence of femoral glands and a derived vomeronasal organ. In addition, previous studies pointed to size differentiation in playing an important role in species’ dispersal capacities and shaping of their geographic ranges. Despite the high phenotypic variation observed in this clade, to date an exhaustive morphological analysis of their anatomy has still not been performed, much less in relation to internal structures. Here, we present a comprehensive skeletal description of a mantellid species, Blommersia transmarina, from the island of Mayotte in the Indian Ocean, which has potentially undergone a process of moderate gigantism compared to other Blommersia species. We describe its intraspecific skeletal variation utilizing non-destructive volume renderings from μCT-scans, and characterize the presence of sexual dimorphism and size covariation in skeletal structures. Notably, we found numerous signs of hyperossification, a novel structure for mantellids: the clavicular process, and the presence of several appendicular sesamoids. Our findings suggest that skeletal phenotypic variation in this genus may be linked to biomechanical function for reproduction and locomotion.