BackgroundPrevious flatworm phylogenetic research has been carried out analysing 18S and 28S DNA markers. Through this methodology, Mariplanellinae subfamily has been recently re-classified as Mariplanellida status novus. This new classification implied that 3 genera belonged to Mariplanellida:Mariplanella,LonchoplanellaandPoseidoplanella. In this study, we aim to clarify some of the relationships within Rhabdocoela analysing 18S and 28S DNA markers of a total of 91 species through Maximum Likelihood and Bayesian Inference methodologies. A total of 11 species and genera, includingLonchoplanella, from the island of Sylt are included and had not previously been involved in any molecular phylogenetic analyses.ResultsOur phylogenetic results support Mariplanellida as an independent group within Rhabdocoela and its status as an infraorder. Our study suggests thatLonchoplanella axibelongs to Mariplanellida. Within Rhabdocoela,Haloplanella longatubais nested within Thalassotyphloplanida, instead of Limnotyphloplanida. Within Kalyptorhynchia, the taxon Eukalyptorhynchia turned out to be paraphyletic including members of Schizorhynchia. These results also support the position of the genusToiaseparate from Cicerinidae.ConclusionsLonchoplanella axibelongs to Mariplanellida, whose status as infraorder is herein confirmed. The genusToiabelongs separate from Cicerinidae. Further research is needed to clarify the phylogenetic relationships ofHoploplanella. Most of the species, genera and families included in this study with more than one terminal are monophyletic and well supported. Adding gene markers and complementary morphological studies will help to clarify those relationships that remain uncertain.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40850-023-00171-y.