A new species of Iberian cyprinid fish, Chondrostoma almacai, from the southwest of Portugal is described. Distribution area includes the Mira, Arade and Bensafrim drainages, previously considered to be inhabited by another phylogenetically related taxon, Chondrostoma lusitanicum. Chondrostoma almacai sp. nov. and C. lusitanicum present important morphological similarities, though significant differences were found for meristic and morphometric characters. The main diagnostic characters for C. almacai are the higher number of scales on the lateral line and above the lateral line, the lower number of right pharyngeal teeth, the longer snout and the smaller head depth. Furthermore, the new species has a small number of gill rakers and a larger predorsal distance, pelvic fin length and eye diameter. Previous molecular data, both mtDNA and nuclear markers (allozymes), suggested that C. almacai and C. lusitanicum are strongly differentiated sister-species. The morphological variability and geographic distribution of C. lusitanicum are reviewed and the most southerly populations from the southwest of Portugal are now recognized as the new species, C. almacai. It is recommended that both species be considered Critically Endangered according to the IUCN Red List Categories and Criteria [B1ab(ii,iii,iv)c(iv)+2ab(ii,iii,iv)c(iv) for C. almacai and A2ce+3ce+4ce for C. lusitanicum].