DNA barcoding has been successfully applied to a very large number of taxa, but remains problematic for basal diploblasts, and debates about suitable molecular markers are ongoing. Sea anemones (Anthozoa: Hexacorallia: Actiniaria) populate most any marine environment and often play an ir- replaceable role as hosts to other animals. Three genetic markers were tested to assess their utility for molecular species identification in members of the Actiniaria, namely the cyto- chrome oxidase subunit I (COI), a COI Intron with a Homing Endonuclease Gene (HEG), and the Internal Transcribed Spacer II (ITS II). Both the power of COI and the COI Intron to distinguish species is limited by events of very low inter-specific sequence differences and not by high intra- specific diversity. This finding implies that more comprehen- sive taxon sampling will not resolve this problem and other markers need to be investigated in several families. Results should discourage the use of ITS II as alternative to COI for barcoding in Actiniarians, since it shows similar limitations to COI.