The study of fishes in aquatic ecosystems is crucial from different aspects, including ethological, ecological, management and preservation of the natural resource, stocks exploitation and aquaculture. Thus, to survey population structure in Mosul bleak (Alburnus mossulensis Heckel, 1843) in ten rivers in Karun River basin, in summer 2009, 195 specimens were captured by a seine net. Twenty-two morphometric characteristics were measured by a digital caliper and 14 meristic characteristics were counted under a binocular. Initially, to remove the size effects caused by allometric growth pattern, values of morphometric characteristics were standardized. Differences between populations were analyzed using analysis of variance (ANOVA), Duncan test, principle component analysis (PCA) and canonical variate analysis (CVA). Lengths of specimens were between 27.9-160.2 mm. Among the morphometrics, 21 and among the meristics, 13 characteristics, were significantly different among the populations (P<0.05). Three first components were responsible for 75.68% of variances in studied populations. Canonical variate analysis showed Khersan, Ivan-e Abbasi and Darband rivers were different from other populations. Beside, although specimens from Bashar and Marbor rivers were overlapping with populations from Banestan, Shirvan, Dopolan, Aligodarz and Sepidar rivers, these three populations were different from each other. The results of this study showed that morphometric and meristic characteristics are able to differentiate Mossul bleak populations from each other.