We investigated the habitat use and feeding ecology of 10 cetacean species encountered along the south-eastern coast of Brazil (24–26°S) using carbon (δ13C) and nitrogen (δ15N) stable isotopes. Hierarchical cluster analysis distinguished two main groups based on their isotopic patterns. One group included migratory baleen whales (Megaptera novaeangliae and Eubalaena australis) with the lowest δ13C and δ15N values, reflecting baseline isotopic values of their Subantarctic feeding grounds and consumption of lower trophic level prey. Resident species and those occasionally occurring in Brazilian coastal waters highly differed from the migratory whales in their isotopic values. In this group, Tursiops truncatus had the highest δ13C and δ15N values, indicating coastal habits and relatively higher trophic position. Similar δ13C values were observed in Sotalia guianensis, Pontoporia blainvillei, Orcinus orca and Steno bredanensis. However, the former two species had lower δ15N values than the latter two, indicating different trophic positions. The relatively lower δ13C values observed in Stenella frontalis suggest greater influence of pelagic prey in their diet. Furthermore, the lower δ13C values observed in Delphinus delphis and Balaenoptera edeni were associated with upwelling events that occur along the region, affecting the isotopic values of their main prey. Juvenile M. novaeangliae had higher δ13C and δ15N than the adults, which may indicate feeding in areas with different isoscapes and consumption of pelagic schooling fish with relatively higher trophic levels than krill. This study provides preliminary information that are useful to understand the habitat use and coexistence of cetacean species occurring in south-eastern Brazil.