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The Lesser Rhea (Rhea pennata), a large flightless bird native to South America, held historical significance as a vital resource for Patagonian hunter–gatherer societies. Despite the species' cultural and ecological importance, the historical population dynamics of R. pennata remain poorly understood. Although present in the archaeological record, its abundance is not consistently documented and the reasons remain unclear. This study investigates the late Holocene population trends of R. pennata using ancient DNA analysis. By analyzing complete mitochondrial genome sequences from dated archaeological specimens, we reveal a significant population increase from 700 to 500 years Before Present (BP), followed by a period of relative stability from 500 to 300 years BP. Subsequently, a subtle decline in population size is observed, coinciding with the arrival of European settlers; however, due to considerable uncertainty in population estimates, definitive conclusions regarding this decline are challenging to make. Historical records indicate heightened rhea hunting during this period, coterminous with a decrease in the abundance of rhea eggshell fragments. It is suggested that climatic factors may have influenced these population dynamics, particularly favoring rhea population growth from 700 to 500 years BP. This study contributes to our understanding of the historical ecology and human‐rhea interactions in Patagonia, emphasizing the importance of interdisciplinary approaches in reconstructing past population dynamics. [ABSTRACT FROM AUTHOR]