Several studies have emphasized the variable abundance of Pygoscelid penguins from different colonies around Antarctica. In this study, the extinction risk of Adélie, Chinstrap and Gentoo penguins was evaluated in order to identify the most endangered colonies under present-day and future environmental scenarios. The extinction risk was estimated for twelve colonies from environmentally contrasting areas, such as the Antarctic Peninsula, Ross Sea and East Antarctica. We focused on the endogenous structure and the response of population dynamics of each colony to exogenous perturbations. The intraspecific competition appears as the most important endogenous factor in all colonies. In turn, the response to exogenous perturbations was rather idiosyncratic and dependant on the local conditions. Those colonies most vulnerable to climate change showed a strong dependency on sea ice extent during the winter, i.e. prior to the breeding season, which directly affects the carrying capacity of the area. The reduction of carrying capacity is mediated by a decrease in food availability and appears as key factor for the persistence of these populations. Based on these results, probabilities for extinction and quasi-extinction under different climate change scenarios were estimated. The most vulnerable Adélie penguin colonies are distributed on the Shetland Islands (Antarctic Peninsula) and at Syowa Station (Eastern Antarctic). The Subantarctic Gentoo penguin colony on Marion Island appears particularly vulnerable and governed by macro-scale environmental variability represented by the Southern Annular Mode index (SAM).