During a recent survey of the zoanthid (Cnidaria: Anthozoa) fauna of Taiwan, specimens resembling Acrozoanthus australiae (family Zoanthidae) were found at Kenting and Green Island, Taiwan, attached to eunicid worm tubes growing out from under large Porites coral colonies in coral reef environments. As this species had previously been described only from eunicid worm tubes in mud flats in Australia and Indonesia, and no studies had specifically examined its phylogenetic position, molecular and morphological examinations were conducted to determine the identity of the Taiwan specimens, and its phylogenetic relationships with other Zoanthidae genera and species. At the same time, endosymbiotic Symbiodinium types within specimens were also investigated. Results from the phylogenetic analyses of sequences of three DNA markers [cytochrome oxidase subunit I, mitochondrial 16S ribosomal DNA, internal transcribed spacer 2 of ribosomal DNA (ITS-2)] strongly suggested that the Taiwan specimens were identical with A. australiae. Based on endosymbiont ITS-2 sequences, these colonies were in symbiosis with Symbiodinium clade D1a (= S. trenchii), theorized to be adapted to both comparatively cold and hot marine environments. Furthermore, phylogenetic analyses from all three zoanthid DNA markers suggest that Acrozoanthus may be within the closely related genus Zoanthus. This study demonstrates the overall lack of data on zoanthid species' distributions, and it is recommended the diversity of zoanthids within the nearby Coral Triangle be investigated to link Indo-Australian zoanthid data with information from Japan and the northwest Pacific. © 2010 Senckenberg, Gesellschaft für Naturforschung and Springer.