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Cichlids are textbook examples for rapid diversification and high species diversity. While in South America, several hundred and in Africa, more than 1500 species of cichlid fish have been described, only one single cichlid species, Iranocichla hormuzensis Coad 1982, was known from Iran, the easternmost range margin of the species-rich African cichlids (Cichlidae: Pseudocrenilabrinae). The aim of our paper was to assess the genetic and phenotypic diversity among populations of Iranocichla across most of its geographical range in Southern Iran. For this, we sequenced two mitochondrial genes and collected color observation of male nuptial coloration in different habitats. Besides conspicuous differences in male nuptial coloration, we found considerable genetic differentiation among Iranocichla populations pointing to the existence of at least two allopatric species, with no evidence of more than one species at one site. Diversification within Iranocichla started, based on our data, in the middle or late Pleistocene and was followed by further population differentiation and bottlenecks during isolation events in the last glacial maximum. Population dispersal leading to the population structure observed today most likely occurred in the course of the early Holocene sea-level rise.