Bioeroding sponges of the Cliona viridis species complex play a large role in carbonate cycling and reef health. In the present study we provide the first record and a description of a Mediterranean lineage of C. viridis (Schmidt, 1862) in the south-western Atlantic. Specimens were collected in Maricás Archipelago, Rio de Janeiro State in September 2010 by scuba diving at 10–12 m depth and deposited in the Porifera collection of Museu Nacional, Universidade Federal do Rio de Janeiro. Morphologically, the specimens presently examined are very similar to those described in the beta and gamma growth form from the Mediterranean. The Brazilian and Mediterranean specimens share large and irregular papillae over 2 cm in diameter, megasclere tylostyles up to 500 µm long and microsclere spirasters with up to five twists and 34 µm long. A Maximum Likelihood analysis of 28S rDNA of C. viridis, C. aprica, C. jullieni, C. schmidti and C. varians was performed for a genetic identification of the Brazilian specimens. The Brazilian material is phylogenetically closer to the Mediterranean C. viridis than to the Caribbean and Indian Ocean members of this species complex included in the present analysis. Our results suggest that C. viridis is a cryptogenic species with a distribution extending from the Mediterranean to the eastern Atlantic and in the SE Brazilian coast or further.