While sympatric species are known to host the same parasites species, surveys contrasting parasite assemblages between sympatric species are rare. To understand how parasite assemblages between sympatric host species differ in a given locality, we used a non-invasive identification method based on high-throughput sequencing. We collected fecal samples from mouse lemurs and sympatric species in Ranomafana National Park, Madagascar, during 2010-2012 and identified their parasites by metabarcoding; sequencing the small ribosomal subunit (18S) gene. Our survey included 11 host species, including: endemic primates, rodents, frogs, gastropods and non-endemic black rats and dogs. We identified nine putative species of parasites between host species, although their correspondence to actual parasite species is not clear as the resolution of the marker gene differs between nematode clades. For the host species that were successfully sampled with ten or more positive occurrences of nematodes, i.e., mouse lemurs, black rats and frogs, the parasite assemblanges differed significantly between host species, sampling sites and sampling years. Our metabarcoding method shows promise in interrogating parasite assemblages in sympatric host species and emphasizes the importance of choosing marker regions for parasite identification accuracy.