For land-breeding marine organisms such as seabirds, knowledge about their habitat use has mainly been gained through studies of breeding individuals that are constrained to return frequently to their breeding grounds. In this study we set out to measure whether: a) habitat selection in the non-breeding period predicts habitat selection in the breeding period, and b) whether breeding individuals concentrated their activity on the closest suitable habitats. Macaroni Eudyptes chrysolophus and gentoo Pygoscelis papua penguins, two marine predators with contrasting foraging strategies, were tracked from the Iles Kerguelen and their habitat selection investigated through Mahalanobis distances factorial analysis. This study presents the first data about gentoo penguins’ juvenile dispersal. For both species, results showed 6.9 times larger maximum ranges and up to 12.2 times greater distances travelled during the non-breeding period. Habitat suitability maps suggested both species made similar environmental selections whatever the period. Macaroni penguins targeted pelagic areas beyond the shelf break while gentoo penguins always remained over the shelf. We consider the ecological significance of larger scale movements made outside the breeding period and suggest that this non-breeding period is of particular interest when attempting to understand an animal's habitat selection.