We examined changes in genetic diversity in populations of two small mammal species inhabiting islands on a lake. We hypothesized that a less mobile species, such as the bank vole, would lose genetic diversity quicker than the yellow-necked mouse, which can more easily cross habitat barriers. In contrast to this we found that the effects of isolation were much more prominent in the case of the mouse than the vole. In the vole population, on the larger island, genetic diversity remained constant over subsequent years in spite of marked isolation. On the smaller island, we noted an increase in genetic diversity which was probably caused by immigration of a small group of individuals. Genetic diversity in the mouse population decreased markedly over the course of the study. In the bank vole, the preservation of genetic diversity, especially on the larger island, may have been possible due to the specific spatial and social organization of this species, which allows the maintenance of a relatively stable number of individuals. In contrast to the bank vole, the lack of territorial behavior in adult females of yellow-necked mice may lead to frequent dramatic seasonal ’booms and busts' in population size and genetic diversity. This can lead to extremely low numbers of mice, which are likely to lead to the extinction of some island populations.