The Persian Gulf harbours a group of islands off the Iranian coast, with known and distinct times of isolation, that are a result of sequential separation from the mainland because of rising sea levels subsequent to the last glaciation. In the present study, we examine the variation in the morphology of Brandt's hedgehogs Paraechinus hypomelas (Mammalia: Erinaceidae), both from these islands and mainland Iran, aiming to evaluate the effects of isolation time and to determine whether it conforms with the island rule. The results highlight a clinal variation along the sampled locations, closely reflecting the progressive historical isolation of the islands from the mainland, and complying with what could be expected given the island rule. The observed levels of morphological differentiation correlate with the timing of the hypothetical last faunal exchanges between Hengam, Larak, and Qeshm islands and the mainland. Additionally, subspecific taxonomy of the species throughout its distribution range in south-west Asia was revised using our extended information alongside available data from the literature. The results show that the large-sized nominate subspecies, Paraechinus hypomelas hypomelas, is distributed throughout mainland Iran to the western side of the Indus River in Pakistan, suggesting the presence of a single subspecies (Paraechinus hypomelas niger) from the entire Arabian Peninsula. Small-sized individuals from the Indus Valley in Pakistan (Paraechinus hypomelas blanfordi) and those from the first isolated island, Larak, clearly deviate from all other samples forming a distinct cluster, which provides a basis for the description of a new subspecies.