Marine ecosystems are becoming increasingly threatened by anthropogenic disturbances, and understanding where marine top predators forage is vital to ecosystem based marine spatial planning. Using habitat models to understand which variables influence the distribution of predators at-sea can enable us to predict the distributions of un-tracked populations, and thus help to identify any potential threats they may face. In the Southern Ocean the expanding krill fisheries have the potential to impact penguin populations. We show that the distribution of chinstrap penguins can be predicted using two simple variables; the distance to the colony and a measure of the direction of travel towards the shelf edge, whilst avoiding high densities of Pygoscelis penguins from other colonies. Additionally, we find that the chinstrap penguins breeding on the South Orkney Islands use areas which overlap with frequently used krill fishing areas. If the krill fisheries continue to expand, then impacts on the penguin populations may become evident. With this in mind, we recommend the implementation of monitoring schemes to investigate the effects of prey depletion on predator populations, and to ensure that management is addressed at spatial and temporal scales relevant to ecosystem operation.