Contrasted phylogeographic patterns on mitochondrial DNA of shallow and deep brittle stars across the Atlantic-Mediterranean area. Previous studies on Ophiothrix in European waters demonstrated the existence of two distinct species, Ophiothrix fragilis and Ophiothrix sp. II. Using phylogenetic and species delimitation techniques based on two mitochondrial genes (cytochrome c oxidase I and 16S rRNA) we prove the existence of a new congeneric species (Ophiothrix sp. III), occurring in the deep Atlantic coast of the Iberian Peninsula and the Alboran Sea. We compared phylogeographic patterns of these three Ophiothrix species to test whether closely related species are differentially affected by past demographic events and current oceanographic barriers. We used 432 sequences (137 of O. fragilis, 215 of Ophiothrix sp. II, and 80 of Ophiothrix sp. III) of the 16S rRNA from 23 Atlantic-Mediterranean locations for the analyses. We observed different geographic and bathymetric distributions, and contrasted phylogeography among species. Ophiothrix fragilis appeared genetically isolated between the Atlantic and Mediterranean basins, attributed to past vicariance during Pleistocene glaciations and a secondary contact associated to demographic expansion. This contrasts with the panmixia observed in Ophiothrix sp. II across the Atlantic-Mediterranean area. Results were not conclusive for Ophiothrix sp. III due to the lack of a more complete sampling within the Mediterranean Sea.