Species delimitation is central to understanding biodiversity and its conservation, yet genetic divergence among sister lineages is often insufficient to demonstrate reproductive isolation or to resolve speciation unambiguously. This limitation is especially pronounced in marine invertebrates such as corals. Their slowly evolving genomes, cryptic diversity, and complex reproductive traits can obscure species boundaries. These challenges also characterize the Paramuricea-species complex occurring in the Iberian-Atlantic, whose members, including those studied here, commonly dominate deep coral gardens. Within this complex, sympatrically occurring yellow and purple morphs exhibit little mitochondrial differentiation, despite evidence of partial genetic structuring. By characterizing gametogenesis, spawning time, and early life-history stages, we reveal pronounced prezygotic barriers between the yellow (broadcast-spawning) and purple (surface-brooding) morphs, including consistent multi-year temporal separation and strongly contrasting fertilization environments. These differences extend into embryonic development, larval morphology, behaviour, and settlement dynamics and reflect divergent dispersal strategies. Overall, our results provide direct biological evidence that the two morphs represent independent evolutionary lineages, supporting their recognition as distinct species. This model system represents a contemporary example of ecological speciation and may serve as a powerful model for future research on the genetic coupling between reproductive modes and life-history traits.

The accurate delimitation of species boundaries in non-bilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondria]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi colour morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.