The deep-sea corals Dendrophyllia ramea and Dendrophyllia cornigera occur in Mediterranean and Atlantic waters. Both species can be found in different environmental conditions, and they can colonise hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a huge knowledge gap on the genetic characteristics of the two species, including on the relationships among these two species and the possibility of cryptic species along their range. The recent discovery of Dendrophyllia populations along the coasts of Cyprus raised new questions in this context. These corals were related to D. ramea but with some morphological differences with other known populations of this species. Here we study the specific status of Dendrophyllia corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis on a pair of Caryophyllia species. Both morphological and genetic data confirm that Cyprus corals belong to the D. ramea species. We then tested speciation scenario with transcriptome data: the results indicate an absence of current gene flow between D. ramea and D. cornigera, and a divergence time older than 3 million years. We discuss the possible historical and ecological factors which may have shaped speciation in these species.