Abstract: The Southern Ocean provides one of the largest environmental gradients on Earth that lacks geographical barriers, and small but highly mobile petrels living there may offer fine models of evolution of diversity along environmental gradients. Using geolocation devices, we investigated the winter distribution of closely related petrel species breeding sympatrically in the southern Indian Ocean, and applied ecological niche models to compare environmental conditions in the habitat used. We show that thin-billed prions (Pachyptila belcheri), Antarctic prions (Pachyptila desolata) and blue petrels (Halobaena caerulea) from the Kerguelen archipelago in the southern Indian Ocean segregate latitudinally, sea surface temperature being the most important variable separating the distribution of the species. Antarctic prions spent the winter north of the Polar Front in temperate waters, whereas blue petrels were found south of the Polar Front in Antarctic waters. Thin-billed prions preferred intermediate latitudes and temperatures. Stable isotope values of feathers reflected this near complete niche separation across an ecological gradient that spans large scales, and suggest evolutionary isolation by environment. In pelagic seabirds that exploit large areas of ocean, spatial niche partitioning may not only facilitate coexistence among ecologically similar species, but may also have driven their evolution in the absence of geographical barriers.