This work aimed to compare hybrid and non-hybrid populations of Hircanian goby (Ponticola hircaniaensis) from two rivers, Kabudval and Shirabad, Golestan Province, respectively. For this purpose, 20 morphometric characteristics were measured. To reveal the morphological differences between the studied populations, the morphological characteristics after standardization were analyzed using Discriminant Function Analysis (DFA) and Non-parametric Multivariate Analysis of Variance (NPMNOVA) based on the P-value obtained from the permutation test with 1000 repetitions. The results of Kruskal-Wallis's test showed that out of 20 morphometric characteristics, 11 traits significantly differ between the two populations. Also, the results of DFA analysis based on the permutation test with 1000 repetitions showed a significant difference in morphology between the two populations of Kabudval and Shirabad rivers (P = 0.048). Since the habitat conditions of the two rivers, Kabudval and Shirabad, both forest streams, are almost identical, the morphological difference between these two populations of Hircanian goby can probably be due to the genetic difference due to hybridization.