Populations that are connected by immigrants play an important role in evolutionary and conservation biology, yet we have little direct evidence of how such metapopulations change genetically over evolutionary time. We compared historic (1894–1906) to modern (1988–2006) genetic variation in 11 populations of warbler finches at 14 microsatellite loci. Although several lines of evidence suggest that Darwin's finches may be in decline, we found that the genetic diversity of warbler finches has not generally declined, and broad-scale patterns of variation remained similar over time. Contrary to expectations, inferred population sizes have generally increased over time (6–8%) as have immigration rates (8–16%), which may reflect a recent increase in the frequency and intensity of El Niño events. Individual island populations showed significant declines (18–19%) and also substantial gains (18–20%) in allelic richness over time. Changes in genetic diversity were correlated with changes in immigration rates, but did not correspond to population size or human disturbance. These results reflect the expected stabilizing properties of whole metapopulations over time. However, the dramatic and unpredictable changes observed in individual populations during this short time interval suggests that care should be taken when monitoring individual population fragments with snapshots of genetic variation.