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Seabirds and their response to climate perturbations are important bioindicators of changes in Antarctic ecosystems. During 30 years of observations of two chinstrap penguin ( Pygoscelis antarcticus) colonies, one on King George Island and the other on Penguin Island (South Shetland Islands, Antarctica), the size of the breeding populations decreased by 84 and 41 %, respectively. We applied analyses of amplified fragment length polymorphisms to study the genetic structure of the two populations and to evaluate the influence of the sudden population decrease. Our data indicate that there were only weak genetic differences between the populations, which were not strong enough to support the hypothesis of population differentiation. Weak genetic differences observed between the two populations seem not to be determined by selection processes. We hypothesize that the very low level of between-population genetic structure can be explained by some extent of genetic drift, which is largely compensated by gene flow. Moreover, the two populations seem to remain in a stationary state. Our results support the hypothesis of limited natal philopatry in chinstrap penguins. The observed decrease in population size is probably caused by emigration or a rise in juvenile mortality due to the increasing krill limitation of the marine food web. However, detailed research is required to address this issue. [ABSTRACT FROM AUTHOR]