Abstract Iran is a major freshwater fish diversity hotspot in the Middle East, and is an important zoogeographical area in west Asia, acting as the crossroads and dispersal corridor between several major biogeographical realms of the world. The topmouth gudgeon, Pseudorasbora parva was first recorded in Iran on 6 May 1991 in the Caspian Sea basin and is now widely distributed across the country. Despite widespread distribution in the Iranian inland waters, its invasion history and genetic background remain unknown. Here, based on the mitochondrial DNA control region (806 bp) sequence variation of 161 P. parva samples collected from 15 Iranian localities and additional sites in Europe and Asia, as well as a cytochrome c oxidase subunit I barcode database (615 bp) including 166 novel and archived sequences, we characterised the pattern of genetic diversity and its colonisation history in Iran. Our results show the presence of three matrilineal haplotypes in Iran belonging to two distinct lineages: (1) a widespread lineage with a common haplotype found throughout the country and one exclusive haplotype confined to the Mashkid basin, whose origin can be traced back to a single introduction of a small number of propagules from Japan and corresponded to the Iranian introduction of P. parva in the late 1980s; (2) a Chinese lineage represented by a single haplotype found in the Shafarood River of the Caspian Sea basin but also translocated to central Iran, penetrated recently to northern Iran through natural dispersal from Azerbaijan as an extension of the European wave of invasion. At the global scale, there is less genetic diversity in west Asia than in Europe and the Asian native range. At the local scale, estimates of genetic diversity in Iranian P. parva populations are extremely low but the Caspian Sea and Esfahan basins gained higher diversities from admixture of highly divergent Japanese and Chinese lineages. Our phylogenetic and species delimitation analyses also suggest the existence of multiple putative species in the native range of P. parva and stress the need of an integrative taxonomical approach based on additional morphological and nuclear DNA data.