Marionina (Michaelsen in Pfeffer, 1890) is a worldwide distributed genus of small enchytraeids living in mainly aquatic habitats. The genus is polyphyletic, including about 100 species with diverse morphological characters and cryptic lineages; therefore, taxonomic revisions were performed recently, and further actions are needed in the future. In our study, Marionina individuals were investigated from decaying seagrass debris collected from seashores in Croatia and Italy using morphological characters and molecular markers involving the COI and H3 genes and the ITS region. Descriptions of two new Marionina species, M. puntaalanensissp. nov. and M. orbiferasp. nov., are presented in this paper, and in addition, the description of a third new Marionina species, M. reichartisp. nov., from the shore of the freshwater Lake Balaton (Hungary) is provided here. All three new species are small (2–3.5 mm in vivo with less than 30 segments), their clitellum is saddle-shaped, the dorsal anterior blood vessel bifurcation is in III, and the spermatheca is attached to the oesophagus. The main diagnostic features of M. puntaalanensissp. nov. are: brain incised posteriorly; dorsal vessel from the clitellar region; two chaetae in all bundles; three pairs of preclitellar nephridia; small subneural glands in XIII–XIV; seminal vesicle absent or small; ectal duct of spermatheca surrounded along the length by glands and one larger. The main features of M. orbiferasp. nov. are: brain truncate posteriorly; dorsal vessel from the clitellar region; two chaetae in all bundles; two pairs of preclitellar nephridia; subneural glands in XIII–XIV; seminal vesicle well developed; the lumen of the spermathecal ampulla is characteristically full with many spherical sperm rolls. In M. reichartisp. nov.: brain incised posteriorly, dorsal vessel origin in XII, maximum five chaetae per bundle, often the middle chaetae slightly smaller than the ental ones, three pairs of preclitellar nephridia, subneural glands absent, spermathecal ampulla globular, ectal duct surrounded along the length by glands, and one large sessile gland at the orifice.