The distribution of fossorial water voles Arvicola terrestris on 15 small islands in the Sound of Jura, Argyll, Scotland, was established and populations were characterized in terms of size, structure and genetic composition (12 microsatellites). The results are compared with similar data from four metapopulations of riparian water voles in mainland Scotland. Water voles occurred on six islands, one of which was occupied in 1994, but not on two islands occupied during the 1960s. Probability of occupancy was significantly associated with proximity to the nearest occupied island. Unlike voles on the mainland, which occupy fragmented patches of exclusively riparian habitat, voles on islands were fossorial and occupied large areas of continuous habitat. Spring population sizes were c. 10 times higher on the islands than colonies of mainland metapopulations. Individuals from three islands were genotyped and these populations had 50% lower levels of microsatellite polymorphism than the mainland metapopulations. Rates of inferred contemporary dispersal among islands separated by 1 km or more of sea were very low, according to large differences among islands in genetic composition, proportions of coat colour types and incidence of skin infection. None the less, the long-term persistence of the island populations is likely to depend on such dispersal. Comparisons between island populations and mainland metapopulations indicate that in both fragmented systems the level of dispersal is the primary factor influencing genetic structure. The low genetic variability in the island populations may reflect either past historical events (founder effect and genetic drift) or present ecology (lack of immigration in closed and temporally fluctuating populations).