Amphibians have traditionally been considered to have low dispersal ability and they have become a model for studies on the effects of man-made habitat fragmentation on genetic variation and population differentiation. This study examined the genetic population structure in the common frog (Rana temporaria) and the common toad (Bufo bufo) in an archipelago of the northern Baltic Sea. Heterozygosity was not correlated with distance of the island from the mainland nor, in R. temporaria, with effective population size based on census estimates. Generally, no inbreeding was detected in island populations. The overall differentiation among islands was weak, but the FST values were significantly larger in R. temporaria (FST = 0.068) than in B. bufo (FST = 0.019). Most of the differentiation was a result of differences among groups of islands, differentiation within them playing a minor role. Thus, assuming Wright's island model of migration, gene flow was rather high among closely located islands, but longer distances seemed to form a slight dispersal barrier for R. temporaria. Strong gene flow within the study area was confirmed by lack of isolation by distance. The estimated effective population sizes in R. temporaria were small, the average being 32 breeding females per island. The results indicate that gene flow between island populations across the matrix of open, brackish-water sea is extensive and suggest that the anurans are well able to disperse in this natural metapopulation system.