Osteological structures of fishes are valuable characteristics in taxonomic and phenotypic plasticity studies to understand their evolutionary trends. In this regard, isolation of populations can lead to morphological divergence particularly in osteological structures which can result in their differentiation. Hence, this study aimed to describe the osteological features of Waspi Cabdio morar and compare its two allopatric populations inhabiting in Makran and Mashkil basins of Iran. For this purpose, 30 specimens were sampled from each basin. The specimens were fixed into 4% buffered formalin after anaesthetizing and then cleared and stained with alizarin red S and alcian blue for osteological examinations. Then the osteological features of this species were described in detail. The results showed that Sarbaz River population possesses less curved haemal and neural spines compared to those of Mashkil which results in a deeper body shape. Also, the Mashkil population had a deeper caudal peduncle due to bifurcated neural spines. In addition differences in features of parietal, parasphenoid, prevomer and branchial arches were observed. The observed morphological divergence may reflect the emerging evolution in response to environmental factors of their habitat and geographical isolation.