Morphometric variation in Aphanius iberus was analysed to demostrate the remarkable genetic divergence between Mediterranean and Atlantic population of Iberia. Four discrete morphotypes in males and three in females were distinguished. Morphometric data discriminated the Atlantic and Mediterranean populations, but revealed the Villena population as the morphologically most differentiated. Atlantic populations were described as a new species, Aphanius baeticus sp. nov., which differs from A. iberus in the overall shape, coloration pattern and number of branched rays on the dorsal and anal fins. The Villena population was retained in A. iberus because, despite of its morphological differentiation, show high genetic introgression at the nuclear genome with neighbouring populations. The range of A. baeticus sp. nov. is restricted to the eight localities of the Atlantic slope of the Iberian Peninsula. This new species should be considered Critically Endangered (CR) according to the IUCN Red List Categories.