Widely distributed Species in different geological and ecological environments often exhibit great intraspecific diversity. Aphaniops stoliczkanus (Day, 1872) is an endemic species of Middle East occurring over a vast geographic range in different basins. This species has been observed in freshwater, brackish water and hot sulphur springs; therefore, its populations are known to exhibit considerable morphological variation. In the present study, we have investigated the poorly studied populations of A. stoliczkanus of the Hormuz and Makran basins of Iran in terms of otolith morphology and morphometrics. According to the results, these populations can be divided into two distinct groups including east and west of the Strait of Hormuz. Our results also provide evidence that there is a relationship between otolith morphology and the environment, serving as environmental factors that may influence the formation of specific regions in the otolith shape. Despite the remarkable morphological similarities among otoliths in geographically close populations of Charak and Chiruyeh, our data purposed that geographically these populations have different dorsal tip shapes in their otolith. In comparison to the data from other studies, the otoliths of Qeshm Island appear to resemble the overall shape of otolith found in Oman very closely. However, it is believed that Qeshm Island population was separated from the Hormuz basin populations during the Holocene Sea level rise. Also, the outcomes of this study provide insights into the potential role of environmental factors in shaping intraspecific diversity and the migration patterns of this species within the Persian Gulf.