Free-living flatworms of the genus Macrostomum are small and transparent animals, representing attractive study
organisms for a broad range of topics in evolutionary, developmental, and molecular biology. The genus includes
the model organism M. lignano for which extensive molecular resources are available, and recently there is a
growing interest in extending work to additional species in the genus. These endeavours are currently hindered
because, even though >200 Macrostomum species have been taxonomically described, molecular phylogenetic
information and geographic sampling remain limited. We report on a global sampling campaign aimed at
increasing taxon sampling and geographic representation of the genus. Specifically, we use extensive tran
scriptome and single-locus data to generate phylogenomic hypotheses including 145 species. Across different
phylogenetic methods and alignments used, we identify several consistent clades, while their exact grouping is
less clear, possibly due to a radiation early in Macrostomum evolution. Moreover, we uncover a large undescribed
diversity, with 94 of the studied species likely being new to science, and we identify multiple novel morpho
logical traits. Furthermore, we identify cryptic speciation in a taxonomically challenging assemblage of species,
suggesting that the use of molecular markers is a prerequisite for future work, and we describe the distribution of
putative synapomorphies and suggest taxonomic revisions based on our finding. Our large-scale phylogenomic
dataset now provides a robust foundation for comparative analyses of morphological, behavioural and molecular
evolution in this genus.