Habitat preference is driven by a complex interaction among behavioural patterns, biological requirements, and environmental conditions. These variables are difficult to determine for any species but are further complicated for migratory marine mammals, such as humpback whales Megaptera novaeangliae. Patterns of habitat use in relation to social organization potentially exist for this species on their wintering grounds. Using an integrated GIS approach, we examined the degree to which spatial patterns of habitat stratification are correlated within different humpback whale group types from 6 years of sighting data (1996–2001) collected on the Antongil Bay, Madagascar, wintering ground. Stratification of humpback whale sightings by behavioural classification showed significant variation in depth and distance from shore. Distribution by depth could not be described as a function of group size but could be described as a function of social organization, with mother–calf pairs showing a strong preference for shallower water compared to all other group types. Group size and social organization seem to be factors in distribution by distance from shore. Significant diurnal patterns in distribution by depth and distance from shore also exist, where mother–calf groups maintain a relatively stable distribution and pairs and competitive groups are the most variable. Patterns of habitat preference on this wintering ground appear to be guided by social organization, where distribution by depth and distance from shore highlight areas critical to conservation.