AbstractKiller whales (Orcinus orca) are highly mobile, large marine apex predators that inhabit all oceans. Despite being the most conspicuous top predator, little is known about their ecology along Patagonia, Argentina. Here, we used carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope analysis of bone and dentine collagen from killer whales (n = 13) stranded in northern Patagonia during the period 1970–2014 to assess their trophic ecology. A model‐based clustering analysis identified three distinct groups related with three large marine ecosystems: the Patagonia (P), Subtropical (ST), and Antarctica (A) groups. Group P (n = 8) is characterized by individuals with high δ¹³C and δ¹⁵N values fitting within the isotopic ratios observed over the Patagonian shelf. Group ST (n = 3) is composed of individuals with high δ¹³C and low δ¹⁵N values, similar to those reported for conspecifics in southern Brazil. Group A (n = 2) is composed of individuals with low δ¹³C and δ¹⁵N values, typical from high latitude areas like sub‐Antarctic/Antarctic waters. The finding of different killer whales' isotopic groups over the Patagonian shelf suggests the existence of individuals or groups exploiting different habitats. Our results expand the limited ecological knowledge for the species while presenting the basis to infer more complex ecological hypotheses.