A more accurate assessment of the true diversity within the genus Squalius on the Iberian Peninsula was made using morphological and molecular characters. A phylogenetic analysis based on the complete sequence of the mitochondrial cytochrome b gene was used to reveal monophyletic groups that had the sufficient evolutionary significance to be regarded as new species. On the basis of genetic and morphological characters, Mediterranean populations from eastern and southern Spain that, in the past, were included in Squalius pyrenaicus are herein described as two new species. Squalhis valentinus sp. nov., the new eastern Spanish species, inhabits the Mijares, Turia, Jucar, Serpis, Bullent, Gorgos, Guadalest, Monebre (Verde), and Vinalopo basins as well as the Albufera de Valencia Lagoon. It is distinguished from S. pyrenaicus by a combination of morphometric, meristic and genetic characters, such as a wide caudal peduncle, low number of scales (8-9/35-39/3), large fourth and fifth infraorbital bones, pointed anterior process of the maxilla, frontal bone widen in the middle, large and narrow urohyal, robust lower branch of the pharyngeal bone. Divergence distances of the cytochrome b in S. valentinus sp. nov. are p = 0.021-0.032 with respect to S. pyrenaicus. In addition, S. valentinus sp. nov. has two diagnostic loci to nuclear molecular markers (IDHP-2 and IDHP-3). Squalius malacitanus sp. nov., the new southern Spanish species, inhabits the Guadalmina, Guadaiza and Guadiaro basins in Malaga Province, in southern Spain. S. malacitanus sp. nov. is distinguished from S. pyrenaicus by a combination of morphometric, meristic and genetic characters, such as narrow caudal peduncle, and high number of scales (7-8/39-43/3). The fourth and fifth infraorbitals are large and the anterior process of the maxilla is not pointed. Frontal bone is not wider in the middle. The urohyal is short and wide and the lower branch of the pharyngeal bone is thin. Divergence distances of the cytochrome b in S. malacitanus sp. nov. are p = 0.078-0.086 with respect to S. pyrenaicus. The distribution range of S. pyrenaicus currently includes the Ebro, Jucar, Segura, Guadalfeo, Guadalhorce, Velez, Guadalquivir, Tinto, Odiel, Piedras, Guadiana, Alportel, Sado, Sorraia, Tajo, Colares, Samarra, Sizandro, Grande, Lis and San Pedro basins.