Pygoscelis penguins are experiencing general population declines in their northernmost range whereas there are reported increases in their southernmost range. These changes are coincident with decadal-scale trends in remote sensed observations of sea ice concentrations (SIC) and sea surface temperatures (SST) during the chick-rearing season (austral summer). Using SIC, SST, and bathymetry, we identified separate chick-rearing niche spaces for the three Pygoscelis penguin species and used a maximum entropy approach (MaxEnt) to spatially and temporally model suitable chick-rearing habitats in the Southern Ocean. For all Pygoscelis penguin species, the MaxEnt models predict significant changes in the locations of suitable chick-rearing habitats over the period of 1982–2010. In general, chick-rearing habitat suitability at specific colony locations agreed with the corresponding increases or decreases in documented population trends over the same time period. These changes were the most pronounced along the West Antarctic Peninsula where there has been a rapid warming event during at least the last 50 years.