Geryon longipes is a crab species that inhabits the muddy bottoms of the middle and lower slopes, as well as bathyal bottoms ranging from 400 to 2000 m in depth. To assess its molecular diversity, a fragment of 572 bp of the COI (Cytochrome Oxidase subunit I) mitochondrial gene was sequenced in eight Western Mediterranean locations. Within the studied area, two oceanographic fronts are present (Almeria-Oran Front and Ibiza Channel). From the 124 sequences obtained, only 7 distinct haplotypes were identified. The population distribution indicated three well-differentiated regions: the Alboran Sea, the Gulf of Vera and the Levantine/Catalan coasts. The molecular diversity was compared with that obtained in the same year for the same gene in Liocarcinus depurator, a crab species that is captured on the continental shelf and upper slope (40 to 500 m). The estimates of molecular diversity parameters for the COI gene fragment were rather similar between both species, but the number of haplotypes was higher for L. depurator. Finally, the obtained COI sequences of G. longipes were compared to those from other populations of the species distribution range, recovered from the DNA repository. Only one additional, different haplotype was reported (Sicily), whereas all the rest were common with those described in our study. Therefore, the COI gene fragment would indicate that all the sequences analysed in the Mediterranean and NE Atlantic belong to the same species, G. longipes.