A new species of the calanoid copepod genus Stephos is described from an anchialine cave on Majorca (Balearic Islands). It occurs in sympatry with S. margalefi, another Balearic endemic differing markedly in body size as well as in the morphology of the fifth legs of both sexes. The new species is extraordinary within its family, the Stephidae, and even within the entire superfamily Clausocalanoidea in displaying a paired arrangement of the reproductive system in the female genital double‐somite. No other member of this cluster of 10 families displays such a primitive condition, all exhibiting different degrees of coalescence or reduction of the genital opercula, pores and ducts. We interpret the condition found in Stephos vivesi sp. nov. as secondary, perhaps derived by loss of the operculum concealing the paired apertures and their subsequent migration and separation on the ventral surface. We take advantage of this discovery to amend the diagnosis of S. margalefi, which was inaccurately described and of which the type material has been lost. This species is unique in the genus in expressing the basal exite seta on the maxillule and in having a 4‐segmented (vs. 5‐segmented) male left fifth leg; the latter condition is the result of the failure to express the inter‐segmental articulation between ancestral segments 3 and 4. In addition, it is the only Stephos with the segment 3 of the male left leg 5 (fused to fourth segment) displaying any armature, viz. a tiny spine on the lateral margin, and a pointed process on the medial margin. We tentatively consider S. balearensis, a third cavernicolous species apparently endemic to Minorca, to be a junior synonym of S. margalefi. The disjunct distribution of this apparently stygobiont species, embracing three different islands of the Balearic archipelago, does not pose any biogeographical problem since all three comprised a single island as recently as 17000 yr BP, at the time of the last glacial maximum when a global marine regression of up to 140 m took place.
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