Emperor penguins (Aptenodytes forsteri) breed on the remote coastlines of Antarctica under the extreme conditions of the polar winter. Consequently, the majority of their colonies have never been visited by humans. Anthropogenic climate change and the associated profound shifts in the Antarctic ecosystem now threaten the survival of the species. Due to the extreme remoteness of these colonies, most current population estimates rely on satellite imagery or aircraft surveys, both of which are subject to considerable uncertainties.,In this study, we investigate for the first time the suitability of aerial drones for determining the population size of emperor penguin colonies. To this end, the Atka Bay colony was surveyed multiple times with an aerial drone during a single breeding season. In addition, we evaluated data from 13 aircraft surveys across 5 emperor penguin colonies in Queen Maud Land collected between 2022 and 2025. Our analysis focused on quantifying observer error and modelling breeding pair numbers based on counts of individuals.,As a result, we provide what are likely the most accurate breeding pair estimates for these colonies to date. We also quantified the distinct influence of ground resolution, lighting conditions, and guano staining on observer error. Our findings demonstrate that drones are highly suitable for surveying local emperor penguin colonies, while also highlighting that deriving breeding pair estimates from the number of individuals at the end of the season remains subject to substantial uncertainty.