Zoanthids of the genus Palythoa are common in coral reef environments worldwide, particularly in the intertidal zone. However, their taxonomy remains problematic, resulting in an incomplete understanding of their diversity. Palythoa caesia Dana, 1846 is found in Fiji, Australia, and the Indian Ocean, while P. tuberculosa (Esper, 1805) has been reported from India, the Red Sea, Singapore, Madagascar, and Japan. The lack of obvious characters differentiating the two species, their wide distributions and high levels of intraspecific variation raise the possibility that these species are in fact one. Based on specimens from Australia, the Red Sea, and Japan, we used three DNA markers (mitochondrial cytochrome oxidase I, 16S ribosomal DNA, and the nuclear internal transcribed spacer region of ribosomal DNA) combined with morphological analyses of tentacle numbers, and cnidae to re-examine the identity of these two taxa. Phylogenetic results showed sequences from all specimens for all markers formed one monophyly, and morphological results showed little differentiation between the two putative taxa. Overall, it is apparent these two taxa are the same species, and the senior synonym P. tuberculosa should be used for specimens for the entire Indo-Pacific region.