The emperor penguin (Aptenodytes forsteri) is highly dependent on sea ice conditions, and future climate change may affect its distribution and numbers. Most studies on the demography and population dynamics of emperor penguins in relation to sea ice characteristics were conducted at a single colony (Pointe Géologie). Several non-exclusive hypotheses have been proposed to explain the dramatic decline of this colony, including changes in sea ice conditions, predation, flipper banding and human disturbance. Here, we report and analyse updated long-term trends in numbers of breeding pairs made at two colonies (Pointe Géologie and Haswell Island) where counts are comparable. Similar changes were observed for both colonies and paralleled changes in sea ice extent. At Pointe Géologie and Haswell Island, populations declined similarly and later growth rates were also similar since the early 1990s for Haswell and early 1980s for Pointe Géologie. The magnitude of the decline was similar between both colonies when numbers of breeding pairs were assessed. This study suggests that a common large-scale environmental factor has probably negatively affected both colonies.