Monitoring the recovery of cetacean stocks in the Southern Ocean has been at the core of IWC activities during the past three decades. Data collection in this area is particularly difficult due to the region’s remoteness, limited seasonal accessibility and presence of sea ice. As a result, distribution patterns and habitat affinities, which are necessary to design population surveys for robust stock assessments, are still insufficiently described. Early attempts to study habitat preferences of cetaceans in the Southern Ocean used descriptive techniques, such as overlaying cetacean sightings with maps of habitat variables and simple correlation analyses. Advances in statistical modelling techniques now provide a promising approach for more sophisticated analyses of habitat requirements by relating sighting data to various environmental variables. While most models developed for the Southern Ocean rely on presence-absence data from line-transect surveys, latest improvements of modelling algorithms extent their applicability to different types of data including presence-only data. Here, we present a habitat suitability model using ship-based presence-only data collected from the Atlantic Sector of the Southern Ocean. Opportunistic sightings of cetaceans have been systematically logged by the nautical officers on board the research icebreaker RV Polarstern during expeditions to the Southern Ocean since 2005. A custom-built software tool “WALOG” is used to ensure a standardized protocol to log cetacean sightings and associated metadata. A maximum entropy approach, Maxent, which is specifically designed to analyse presence-only data and ranks amongst the highest performing modelling algorithms, was used to model summer distributions of humpback (n=73) and minke (n=81) whales. The environmental parameters such as water depth, sea surface temperature, sea ice concentration, as well as their derivatives and isopleths were obtained from remote sensing data providers. Probability of presence was modelled using 25% of the data as test data and the remaining 75% as training data. We present distribution patterns and habitat affinities of humpback and minke whales in the Atlantic Sector of the Southern Ocean and discuss whether oceanographic data are representative proxies in describing cetacean distribution in our study area.