The microturbellarian flatworm Gyratrix hermaphroditus (Kalyptorhynchia: Polycystididae) has long been hypothesised to constitute a vast species complex, a view recently confirmed by molecular evidence. However, to date, the complex has not yet been formally split, as its taxonomy is complicated by multiple nested species hypotheses and by the fact that distinguishing features often consist of very subtle morphological differences in the sclerotised male copulatory organ. Here, building on the existing molecular framework, we present a large integrative effort to resolve the species complex. We add new DNA sequences from specimens collected near the type locality of G. hermaphroditus, expand the previously published morphometric dataset with additional measurements and statistical analyses, and use Scanning Electron Microscopy (SEM) to visualise and clarify morphological differences within the complex. As such, we delineate 14 species of Gyratrix, originating from freshwater, brackish, and marine habitats across the taxon’s global range. Species boundaries are primarily defined by variation in the morphology of the copulatory organ, which is especially evident in the high-resolution SEM images. These morphological differences are robustly supported by molecular and morphometric evidence. Finally, we assess the practical value of our new delineations by testing whether they enable reliable identification of both historical and newly collected specimens in the absence of molecular data.