Within flatworms, the vast majority of parasitism is innate to Neodermata, the most derived and diversified group of the phylum Platyhelminthes. The four major lineages of Neodermata maintain various combinations of life strategies. Their evolutionary trajectories have remained molecularly unresolved because of conflicting evolutionary inferences and a lack of genomic data. Here, we generated transcriptomes for nine early-branching representatives of Neodermata and performed detailed phylogenomic analyses to address these critical gaps in our understanding of the evolution of the group. This is the supplementary data to the article “Transcriptomic investigation of parasitic platyhelminths provides a novel understanding of the evolution of endoparasitism and complex life cycles”. It consists of the initial rnaSpades assemblies for the data generated within this study, PhyloFisher database files limited to the Obazoa taxa, alignments and tree files relevant to the analyses that appear in the publication.