coralligenous assemblages are among the most species-rich and vulnerable habitats of the Mediterranean Sea. Nevertheless, data on connectivity patterns on species inhabiting these habitats, crucial to define management and protection priorities, are largely lacking. Moreover, unreliable species-level taxonomy can confound ecological studies and mislead management strategies. In the northwestern Mediterranean two Parazoanthus axinellae morphotypes differing in size, color and preferred substrate are found in sympatry. In this study, we used COI and ITS sequence polymorphism to assess (1) the genetic divergence between the two morphotypes, (2) their connectivity patterns and (3) their phylogenetic position within the Parazoanthidae. Specimens of P. axinellae were sampled in 11 locations along the northwestern Mediterranean; in 6 locations, samples of the two morphotypes were collected in sympatry. Small genetic diversity and structure were found within morphotypes, while marked and consistent differentiation was detected between them. Moreover, the less widespread morphotype appeared to be closer to Pacific species as P. juanfernandezii and P. elongatus. Our findings confirmed the limited knowledge on Parazoanthus species complex, and how this gap can have important implication for the conservation strategies of this widespread and valuable genus in the Mediterranean Sea. Biogenic reefs are made by calcareous encrusting algae and animals that change the geological primary habitat on which they settled through superimposition of their skeletons. They are among the most productive and diverse benthic ecosystems, providing habitat, feeding grounds, recruitment and nursery areas for a variety of invertebrate and vertebrate species 1. In the Mediterranean Sea, the main biogenic reefs are the coralligenous reefs. They are among the most important Mediterranean ecosystems due to the high diversity of species and ecological processes that they support 1,2. These complex habitats are threatened by several human activities (e.g. recreational fishing and trawling, sediment deposition, anchorage, diving), which lead to their fragmentation and loss 3,4. Monitoring spatio-temporal changes in species composition is crucial to quantify human-induced biodiversity loss and habitat fragmentation, but the absence of clear taxonomic identifiers to distinguish between species makes this a challenging task. Many relevant coralligenous taxa (e.g. Porifera, Echinodermata, Cnidaria) lack diagnostic morphological characteristics, and therefore these groups are recognized as taxonomically problematic, in particular at lower taxonomic levels 5. Moreover, in these species, with high morphological plasticity 6 , some characters such as shape and coloration might not be reliable for species delimitation. It happened that morphospecies have turned out to be a single morphologically variable species 7-9 , and, conversely, what was thought to be multiple growth forms of a single species turned out to be a complex of species 10,11 .