The Gobiidae are one of the largest families of fish in the world. This study aimed to investigate the morphometric characteristics of the specimens belong to three species from Gobiidae family, i.e. Acentrogobius dayi, Bathygobius meggitti and Istigobius ornatus from Makran coast, South-East of Iran. A total of 56 specimens from three Tis, Lipar and Darya-Bozorg stations during the spring and summer of 2018 were captured and transplanted to the laboratory. 36 morphological variables were analysed (including univariate and multivariate), using SPSS and PAST software. The results showed that there was a significant difference between the studied species, mainly in head and pectoral fins. But other characters were not significantly different. The results of cluster analysis showed that B. meggitti was considerably different from the others. This study also demonstrait significant intra-specific differences regarding I.ornatus species. These differences moreover than the head and pelvic fin , were seen in the tail fin. In A. dayi species, intra-specific differences, same as what observed at inter-specific level, were mainly in the head and pelvic fin’ part. A multivariate analysis of  the characters and pairwise comparision of the populations of two species I. ornatus and A. dayi showed that the populations of Lipar and Darya-Bozorg stations in both species are more similar than others. An advanced molecular study as a complementary study can help to clarify species diversity and taxonomy of these poorly known family.