This study was conducted to compare the morphological characteristics of Ponticola iranicus populations from the Anzali Wetland drainage (wetland and its two draining rivers, namely Siahdarvishan and Pasikhan, Southern Caspian Sea basin). For this purpose, five specimens of P. iranicus from the Pasikhan River, 10 from Siah-Darvishan River and 8 from the Anzali Wetland were collected. After anesthesia, fish were fixed into 10% buffered formalin and transferred to the laboratory for further study. A total of 22 morphometric traits were measured using a digital caliper. The data, after removing size, were analyzed for normality and the significant data were selected and used for multivariate analysis, including Principle component analysis (PCA), Canonical variate analysis (CVA) and Non-parametric multivariate analysis of variance (NPMANOVA). The results showed a significant difference in inter-orbital distance, minimum width of the caudal peduncle and eye diameter between the studied populations (P<0.05). In addition, the Anzali wetland population was discriminated from others due to morphological characteristics. The observed morphological changes in P. iranicus can be as a result of their habitat adaptation such as current type and feeding.