The morphometric analyses and genetic variability assessed by RAPD markers have been used to analyse relations among six Serapias taxa from Croatia (S. istriaca, S. pulae originally described as hybrid, S. ionica, S. vomeracea, S. lingua and S. cordigera). S. istriaca distributed in southern Istria and the island of Lošinj and S. pulae stenoendemic taxon distributed only in southern Istria S. ionica is endemic to the Ionian and Dalmatian islands, while the remaining taxa are more widely distributed. The obtained results shows that the endemic S. istriaca is a well characterised taxon, that S. pulae is a hybrid between S. istriaca and S. lingua and that the hybrid is morphologically and genetically more similar to S. lingua than the second parental species S. istriaca. The division into the subsections Steno-, Medio- and Platypetalae is founded based on the floral morphology while the division into the sections Serapias and Bilamellaria is not evident in the quantitative morphological and genetic analyses. Furthermore, considerable genetic resemblance between S. vomeracea and S. ionica was established.