The present study is in agreement with the hypothesis that the variation of ecological conditions in three rivers in northern Israel—the Dan, Hasbani and Hermon Rivers—affects the genetic variations of the species Capoeta damascina. Using mitochondrial DNA (mtDNA), cytochrome b gene (Cytb), 16S and nuclear DNA (nDNA), and Random Amplified Polymorphic DNA (RAPD), four different clusters were found in the Cytb of the Hasbani and Hermon Rivers and only two in the Dan River. Moreover, the clusters in the Hasbani River differed from those found in the Hermon River. A similar result was found when an analysis was made of a different sequence from five different haplotype frequencies using the MegAlign program, the lowest being in the Dan River (only two haplotypes) and the highest in the Hasbani River (four haplotypes). The analysis of molecular variance of Cytb and 16S (AMOVA) for individuals of C. damascina from eight populations in northern Israel showed significant differences between the rivers and the populations. The analysis by mitochondrial 16S of haplotype frequencies of C. damascina populations in the rivers in northern Israel was very low compared to Ctb. Sixteen different haplotypes were found in the different rivers: eight in the Hasbani River, seven in the Dan River and only five in the Hermon River.