Understanding how species can form and remain isolated in the marine environment still stimulates active research. Here we study the differentiation and the possibility of hybridization among three temperate octocorals: Eunicella cavolini, Eunicella singularis, and Eunicella verrucosa. Morphologically intermediate individuals have been observed between them. Among these three species, E. singularis is the only one described in mutualistic symbiosis with photosynthetic Symbiodiniaceae. The symbiosis between Symbiodiniaceae and scleractinian corals is well studied, especially in the context of the response to anthropogenic climate change. Nevertheless, the potential role of symbiotic interactions in speciation processes remains unknown in cnidaria. We tested here the possibility of hybridization between symbiotic and non-symbiotic Eunicella species. Through multivariate analyses and hybrid detection, we prove the existence of on-going gene flow between E. singularis and E. cavolini, with the observation of F1 and F2 hybrids, and backcrosses. Demographic inferences indicate a scenario of secondary contact between these two species. Despite current gene flow, these two species appear genetically well differentiated. Our data also suggest an intermediate abundance of Symbiodiniaceae in the hybrids of the two parental populations. We discuss the evolution of the Symbiodiniaceae/cnidarian symbiosis in the light of our results.