Since the inclusion of molecular data in modern phylogenetic analyses, significant progress in resolving the origins and radiation of flatworms has been made, although some key problems remain. Here I review developments in the supply and use of systematic characters that provide the basis for diagnosis and phylogeny reconstruction, that in turn have driven systematic revisions and the interpretation of broader evolutionary patterns and processes; focus is placed on the parasitic taxa. Although useful tools have been refined to the point of becoming established systematic markers of broad utility, attention to the need for denser gene and taxon sampling is addressed in the light of unresolved questions and current trends in molecular systematics, from nucleotide to genome. Tradition and the nature of available comparative information tends to dictate the choice of systematic markers, but faced with incongruent phylogenies, the emergence of new technologies and the need for rapid species diagnosis, there is a pressing need to assess and standardize our choice of tools so they are fit for purpose, available to all and used widely. I present a brief review of existing and potential sources of phylogenetic characters and discuss their likely value in the context of the systematics and diagnostics of parasitic flatworms.