The precise and repeatable identification of species as independent units of evolution is necessary for any assessment of the structure and evolution of biological systems; particularly in symbiotic systems where specific interactions strongly influence the fitness of species. Symbiotic zoanthids (phylum Cnidaria, class Anthozoa, order Zoanthidea) form associations with at least five different phyla and have global geographic and bathometric distributions; however, the simple morphology of zoanthids challenge our ability to differentiate between intraand inter-specific variation, and endemic and cosmopolitan species. The internal transcribed spacer (ITS) region of the ribosomal RNA nuclear gene was amplified from zoanthids collected from 10 different locations throughout the wider Caribbean region. Hypervariable ITS sequences provide highly informative molecular markers, but are not often fully exploited because of difficulties in sequence alignment. Rather than discarding difficult-to-align

hypervariable regions, I retained all nucleotides by treating blocks of unambiguously aligned sequence as if they were separate genes in a concatenated multi-gene alignment with incomplete taxon sampling for each gene. Sequence alignments were subjected to maximum-likelihood and Bayesian phylogenetic analyses and species where assessed by applying a history-based phylogenetic species concept to the resulting topologies. Phylogeny-based species delimitations have strong concordance with morphologically-defined species and reveal additional species that were not previously recognized.