Abstract The diagnostic features of otolith morphology were provided for the clupeid fishes of the Iranian brackish and marine resources to be used as diagnostic features for the identification of clupeids diversity in these regions. Fish individuals belong to 20 species belong to 13 genera, and four families were collected from the Caspian Sea, the Persian Gulf and the Makran zone of the Oman Sea. Overall, seven otolith morphotypes were distinguished, that is lanceolated (45%), fusiform (20%), boot‐like (15%) and clamp‐like, pentagonal, elliptic and rectangular (each 5%, respectively). The univariate analysis showed that all variables except shape index [sulcus area (SS)/otolith area (OS)] and ROx (roundness) were significantly different among the clupeid species. The interspecific relationships of the otoliths were analysed based on the data of otolith morphology and otolith shape indices. Both dendrograms showed somehow an obvious separation among the studied species. However, the interspecific relationships in the dendrogram based on the otolith morphology have a better resolution. These phenotypic relationships based on otolith morphology among the studied clupeids are largely consistent with the previous hypothesis on the systematics of these fishes and emphasized that the morphological and morphometric features of the otolith, which are highlighted in this study, could be adequately used as diagnostic features for the identification of clupeids diversity.