This study was undertaken to determine the taxonomic position of Isfahan chub using the molecular and morphological data of the fish varieties found in Zayanderud river basin in Isfahan, Iran. For the purposes of this study, 30 specimens of fish were taken from the Cheshmeh-Dimeh area using a Sein Net fishing apparatus. The sequence ofcytochrome b gene as well as the morphological characteristics for all samples were determined. Then, we used 25 morphometric attributes and 7 meristic factors to compare the relative characteristics of the samples with the holotypes of Alburnus and Petroleuciscus, using a one-sample T test.In comparing the samples with the Petroleuciscus genus , 18 factors, out of the 33 relative measurements, showed significant differences ( P 0.001); and, in comparison with the Alburnus holotype, 16 factors, out of the 26 relative measurements, showed significant difference ( P 0.001). Therefore, the results of this statistical analysis appeared to be inconclusive for the purpose of determining the taxonomical characteristics of the target species.In conducting our molecular studies, DNA were extracted from the caudal fin of fish specimens, using the phenol chloroform method, and the quality of DNA samples were evaluated using agarose gels. The PCR treatments were run at an annealing temperature of 60C using a cytochrome b gene (1142 bp) primer pair, and the relevant phylogenetic tree was drawn using the Maximum Likelihood method by using MEGA5.2 software. The resulting dendrogram placed our target species in a sister group with Alburnus fillipi and Alburnus chalcoides. The Alburnus species were determined to belong to three main clades : Clade A included A.alburnus, A.strumicae, A.hohenackeri, A.escherichii, A.scoranza, A.belvica and A.arborella species; Clade B included Alburnus sp (the samples sequenced in this study), A.filippii and A.chalcoides and Clade C included A.orontis, A.balaki, A.kotschyi and A.mossulensis . The results of this study changed the taxonomical order of this genus in such a way that the target species showed no proximity to Petroleuciscus . Interestingly, our research seemed to refute the results of previous taxonomical studies on this species based on its morphology, and appeared to confirm the presence of Alburnus species in Zayandehrud. The results of complete sequencing of c ytochrome b gene indicated that this approach may be much more suitable for taxonomical placement of local species of Iran. Furthermore, considering the usual shortcomings of morphology based methods, the approach taken in this study may prove useful for presenting a more accurate picture of the ecological diversity in aqueous ecosystems of Iran. Keywords: Cyprinidae, Systematic, Morphological characteristics, Genetic taxonomy, Cytochrome b gene