The microscopic members of the genus Urodasys are easily recognizable due to their exceptionally long tail. There are 17 described species within this iconic genus, each distinguished by various sexual organ arrangements and reproduction modalities, including the sole known ovoviviparous gastrotrich species. The remarkable variety in reproductive characteristics has captured the interest of researchers aiming to illuminate its origin and evolution. The recent discovery of a species bearing a novel set of reproductive structures has challenged early hypotheses. However, all the evolutionary scenarios put forward need to be more convincing. To gain deeper insight into the evolutionary history of these iconic animals, we obtained the nucleotide sequence of two nuclear genes and one mitochondrial gene from species’ representatives of the four known possible combinations of the reproductive apparatus and reproduction modalities. The multi-gene data matrix was analysed phylogenetically using three approaches. The analyses yielded phylogenetic trees with invariant topology. In all cases, the specimens appear organized in four robustly supported clades and subclades that reflect their reproductive system organization. Our results suggest that the sclerotized stylet evolved inside the copulatory organ before the loss of the left testis and offers a new scenario for the evolutionary history of genus Urodasys.