Trematodes are parasitic flatworms that usually have a snail as an intermediate host and a vertebrate as final host. They are best known for their medical and economical importance as they cause various snail-borne diseases such as schistosomiasis, a neglected tropical disease affecting more than 200 million people worldwide. The Trematoda are a highly diversified and speciose group of organisms (~18 000 species described), where cryptic species abound. Knowledge on the biodiversity of freshwater trematodes and drivers of their evolutionary diversification remains limited, including for ancient lakes where also the diversity of potential host snails is substantial. As in other parasitic organisms, host diversification and host switching have been put forward as important drivers of speciation in trematodes. Yet, testing this hypothesis is hampered by fragmentary knowledge of the helminth fauna of freshwater snails and the lack of molecular data for phylogenetic analyses. These limitations somewhat reflect research effort, but mainly the lack of tools to detect and identify these parasites directly from their hosts. To tackle this issue, we are developing a new tool based on multiplexing, pooling and next-generation-sequencing of nuclear and mitochondrial genetic markers targeting the snail hosts and their parasites simultaneously. This tool, genotyping by deep amplicon sequencing, will increase the genomic coverage and thus the power to conduct phylogeographic and phylogenetic analyses. Applied to the study of trematodes hosted by populations of snails this tool has the potential to help disentangling the drivers of parasite diversification, snail-parasite co-evolution, and the ecological context of transmission of snail-borne diseases.