PurposeDespite Madagascar’s high amphibian diversity of more than 400 species, only a few polystome species are known from the island. The dissection of frogs from museum collections, together with amphibian and parasite surveys conducted in Madagascar led to the discovery of an undescribed polystome infectingAglyptodactylus madagascariensis. The purpose of this study is to formally describe this species.MethodsPolystomes recovered fromA. madagascariensiswere stained (Acetocarmine) and mounted (Canada balsam) to facilitate morphometrics and taxonomic drawings. Some specimens were fixed in absolute alcohol, a Bayesian tree inferred from the analysis of concatenated 18S, 28S and COI gene sequences was constructed and pairwise distances were calculated. Parasites collected from archived hosts in museums were used for histology and scanning electron microscopy (SEM).ResultsPolystomes recovered fromA. madagascariensisdisplay characteristics of the genusMetapolystomaand morphologically differed from all other known metapolystomes. The Bayesian phylogeny shows thatMetapolystoman. sp. ex.A. madagascariensisandM. falcatumare sister species with high Bayesian posterior probability. Histological and SEM investigations contributed to morphological descriptions.ConclusionsMorphological examination supported by phylogenetic analysis and genetic divergences revealed distinct differences from all known metapolystome species, supporting the description of a new species. Differences between the life cycles ofMetapolystomaandPolystomaprovided additional evidence for the validity of that genus as taxon. WhereasPolystomamay display ovoviviparity on rare occasions after incomplete egg expulsion towards the end of the breeding season,Metapolystomadisplays true ovoviviparity. We emphasize the need for parasite surveys in Madagascar and recommended for museum material to be examined for polystomes to provide supplementary material and localities for further field investigation.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1007/s11686-023-00668-z.