Pseudophoxinus a freshwater fish genus shows remarkable diversification with high number of endemic species in Anatolia. Most of the species of the genus are categorized as endangered for conservation in IUCN Red List due to water abstraction and habitat destruction. The aim of the study is to investigate genetic and morphological structure of Pseudophoxinus populations using allozyme, microsatellite markers and geometric morphometrics (eight landmarks). Sample collection was performed from eight localities for four different Pseudophoxinus species (P. Crassus, P. battalgili, P. egridiri, P. sp) in Anatolia in 2006. Genetic variation was assessed by using six microsatellite and ten allozyme loci. In total, 39 alleles for allozymes and 103 alleles for microsatellites were encountered in all populations. Mean observed heterozygosity was found in the range of 0.0143-0.0875 in allozymes and 0.146 to 0.463 in microsatellites. Significant morphological and genetic differentiation was measured among P. Crassus populations that may indicate to be considered different units in conservation action plans. There was no population differentiation detected by morphological and genetic measurements among P.battalgili populations. Bayesian individual assignment from Structure software revealed that P. battalgili populations are highly mixed in four sampling areas.