The Napo River basin, which is situated within the Upper Amazon archaeological region, is one of the most speciose forests in Greater Amazonia. Standard thinking in scholarship and science holds that these forests are essentially pristine because any Indigenous impacts in the past would have been minimal, seedbanks would have been nearby, and natural forests would have reappeared after the humans left, died out, or dispersed. Inventory research in 2019 on three ridgetop forests in Waorani territory inside the Curaray basin (which drains to the right margin of the Napo River) and a comparable inventory on one control site forest along the Nushiño River (also in the Curaray basin) show human impacts from about the late nineteenth century to about 1960; they occurred during the period of wartime among Waorani themselves and between Wao people and outsiders. The human impacts resulted in the high basal-area presence of two long-lived species with important Waorani cultural uses: cacao (Theobroma cacao L.) and ungurahua palm (Oenocarpus bataua Mart.). These species have high frequency and dominance values and do not occur in the control site, which is comparable in terms of elevation above the flood zone of the rivers in the sample. These findings mean that alpha diversity in the right margin sector (or south) of the Napo River basin cannot a priori be explained by reference to traditionally, biologically accepted patterns of ecological succession but may require knowledge of historical patterns of Indigenous land use and secondary landscape transformation over time due to human (specifically Waorani) impacts of the past.