The Olkhon mountain vole (Alticola olchonensis) is an endemic species of the Lake Baikal area with an extremely restricted range. We investigated the pattern of differentiation of cranial shape and size in five isolated insular populations of A. olchonensis from the Baikal islands (Olkhon, Hubyn, Borokchin, Ogoy, and Zamogoy). The ventral aspect of the cranium was analysed using landmark-based geometric morphometric methods While the sexes of A. olchonensis did not differ regarding cranium size and shape, multivariate statistical analyses showed that there were inter-island differences in skull morphology. Voles from the four small islands were similar in cranium size; the large skull size of voles inhabiting the Olkhon Island may be due to the more favourable habitat conditions on Olkhon. Shape differences among island populations were not associated with the geographic distances between islands. The voles from Borokchin Island differ the most in skull shape compared to other island populations. The combination of reduced gene flow among island populations (due to isolation and drift during population fluctuations) may be a suitable explanation for the significant differences in skull shape among island populations of A. olchonensis.