The genus Alburnus (family: Cyprinid) is a poorly differentiated taxonomic complex that comprises a freshwater fish in the large Eurasian realm with the Inland Systems of Turkey as their component. The given research aims to carry out the comprehensive morphological and genetic description of the Alburnus species living in the Kızılırmak River Basin (Central Anatolia, Turkey). Along the Kızılırmak River, which is the longest river that exclusively flows within the Turkish borders, a variety of freshwater species can be found and several taxa of the Alburnus are also found but these are not well described due to high phenotypic plasticity and scarcity of molecular data. Combining morphometric and meristic analyses with the mitochondrial DNA sequencing (cytochrome b), this study intends to clarify the taxonomic uncertainties and determine phylogenetic relations between populations. Furthermore, the findings indicate that geographical isolation, fragmentation of the rivers, and historical climatic events could have been responsible for speciation in the basin. This study offers useful information on biodiversity and taxonomy of Alburnus species of one of the most ecologically significant freshwater systems in Turkey. It reminds the importance of using both morphological and genetic methods at once to find a species accurately and to define biodiversity. These findings are significant to conservation biology especially when considering anthropogenic pressures such as habitat alteration, pollution as well as global warming which undermine freshwater systems in the area. Further studies should increase the area of study and use nuclear DNA markers to define the phylogenetic relationships and conservation status of the Alburnus taxa in the neighboring countries of Turkey more precisely.