Many ecosystems of conservation concern owe their unique characteristics to long-term management by indigenous peoples. However, there are serious debates concerning the degree and extent of this influence. We argue that delving into the long-term history of a system by compiling research from multiple disciplines helps ecologists to understand the key drivers of ecosystem structure and dynamics, including the role of humans. We use a case study of the endangered Garry oak ecosystem of southern British Columbia (Canada) to show how considering an extended timeline can reveal surprises that challenge conceptions of the way an ecosystem functions. In this system, ecological experiments have shown that the current dominance of exotic species is not due to competitive superiority, but a result of habitat fragmentation and changes in herbivory and disturbance regimes since European settlement. Historical and ethnographic research point to the purposeful and regular use of fire by the Coast Salish peoples of this region, and land survey records indicate that Garry oak has not always been the prime savannah tree species. Paleoecological studies document the maintenance of open savannah habitat in the late Holocene despite cooler, wetter climatic conditions that favour coniferous forests, suggesting a very long history of indigenous management. Archaeological evidence confirms the prolonged presence of human societies on the landscape. These insights contribute both to improved ecological theory and better restoration strategies, and show that ecosystems created via long-term human management are equally valid targets for conservation as ecosystems that have experienced less human influence.