The anadromous Rutilus kutum Kamenskii, 1901is the most important fish in north of Iran with the highest economic value. Ignoring the natural process of reproduction due artificial propagation, catching some migrating broodstocks from the sea (not from the estuaries) and mixing the produced fingerlings in culture ponds within restocking programs in the last 30 years have caused an uncertainty about homing success and population differentiation in the fish. A 13-landmark morphometric truss network system was used to investigate the hypothesis of homeward migration success and population differentiation, while the previous studies revealed low genetic variability among the fish populations. A total of 504 adult specimens were caught from four localities along the southern Caspian Sea in the reproductive period. Univariate analysis of variance showed significant differences among the four groups for 78 standardized morphometric measurements. In linear discriminant function analysis (DFA), the overall assignments of individuals into their original groups were 73.3 % and 80.3 % in males and females, respectively. The principal component analysis (PCA) and clustering analysis based on Euclidean square distances showed that the 504 examined specimens grouped into distinct areas. The results showed that each sampling site represents independent population which confirmed the success of homeward migration. The high grouping ranges suggests that almost all populations return to their birthplace river to breed, which results in high inbreeding. The results can be interesting for management and conservation programs of this valuable species in the Caspian Sea.