Human land-use effects on species populations are minimized in protected areas and population changes can thus be more directly linked with changes in climate. In this study, bird population changes in 96 protected areas in Finland were compared using quantitative bird census data, between two time slices, 1981-1999 and 2000-2009, with the mean time span being 14 years. Bird species were categorized by distribution pattern and migratory strategy. Our results showed that northern bird species had declined by 21 per cent and southern species increased by 29 per cent in boreal protected areas during the study period, alongside a clear rise (0.7-0.8 °C) in mean temperatures. Distribution pattern was the main factor, with migratory strategy interacting in explaining population changes in boreal birds. Migration strategy interacted with distribution pattern so that, among northern birds, densities of both migratory and resident species declined, whereas among southern birds they both increased. The observed decline of northern species and increase in southern species are in line with the predictions of range shifts of these species groups under a warming climate, and suggest that the population dynamics of birds are already changing in natural boreal habitats in association with changing climate.