AbstractThe Middle East contains a great diversity of Capoeta species, but their taxonomy remains poorly described. We used mitochondrial history to examine diversity of the algae‐scraping cyprinid Capoeta in Iran, applying the species‐delimiting approaches General Mixed Yule‐Coalescent (GMYC) and Poisson Tree Process (PTP) as well as haplotype network analyses. Using the BEAST program, we also examined temporal divergence patterns of Capoeta. The monophyly of the genus and the existence of three previously described main clades (Mesopotamian, Anatolian‐Iranian, and Aralo‐Caspian) were confirmed. However, the phylogeny proposed novel taxonomic findings within Capoeta. Results of GMYC, bPTP, and phylogenetic analyses were similar and suggested that species diversity in Iran is currently underestimated. At least four candidate species, Capoeta sp4, Capoeta sp5, Capoeta sp6, and Capoeta sp7, are awaiting description. Capoeta capoeta comprises a species complex with distinct genetic lineages. The divergence times of the three main Capoeta clades are estimated to have occurred around 15.6–12.4 Mya, consistent with a Mio‐Pleistocene origin of the diversity of Capoeta in Iran. The changes in Caspian Sea levels associated with climate fluctuations and geomorphological events such as the uplift of the Zagros and Alborz Mountains may account for the complex speciation patterns in Capoeta in Iran.