Interspecific hybridization has been proposed as a possible explanation for the incredible diversity seen in reef-dwelling corals, but until now little proof of such hybridization in other reef-dwelling anthozoans has been reported. Without further observation of hybridization, the question of such a phenomenon being widespread in Anthozoa remains. Here we have examined the mitochondrial cytochrome oxidase I gene (COI) and the nuclear internal transcribed spacer of ribosomal DNA (ITS-rDNA) from three species of the mass-spawning, encrusting anemone genus Zoanthus (Z. sansibaricus, Z. kuroshio, Z. gigantus) to investigate possible hybridization. The three species coexist at two of three sampling locations in southern Japan. Zoanthus spp. ITS-rDNA region spacers (ITS-1 and ITS-2) were shown to have very high rates of divergence. At locations where all three species co-existed, several of our sampled Z. sansibaricus individuals (with identical “sansi” COI sequences) possessed two very divergent (i.e., species-level difference) ITS-rDNA alleles, the expected “sansi” allele and the divergent “B” allele. Additionally, two Z. sansibaricus individuals possessed only “B” alleles despite having “sansi” COI sequences. These results indicate that Z. sansibaricus has possibly experienced interspecific hybridization at least once with a Zoanthus partner possessing the “B” allele, and that these resulting hybrids may also sexually reproduce, demonstrating potential hybridization occurring in the order Zoantharia (Hexacorallia).