The shallow water sea anemone Phymanthus crucifer exhibitsthree distinct morphotypes, characterized by the presence or absence ofprotuberances on the marginal tentacles, as well as intermediate forms. Thetaxonomic status of the different morphotypes and the diagnostic value ofprotuberances on the tentacles have been debated for this species and thefamily Phymanthidae. We analysed the external and internal anatomy, cnidaeand three mitochondrial molecular markers for representatives of each of thethree morphotypes. In addition, we address the putative monophyly of thefamily Phymanthidae based on molecular data. With the exception of theprotuberances, our morphological and molecular results show no differencesamong the three morphotypes; thus, we consider this feature to beintraspecific variability within P. crucifer. Furthermore,molecular data reveal that the family Phymanthidae is not monophyletic. Inaddition, we discuss several diagnostic morphological features of the familyPhymanthidae.