The origins and lifeways of the inhabitants of Rapa Nui (Easter Island), a remote island in the southeast Pacific Ocean, have been debated for generations. Archaeological evidence substantiates the widely accepted view that the island was first settled by people of Polynesian origin, as late as 1200 CE [1-4]. What remains controversial, however, is the nature of events in the island's population history prior to the first historic contact with Europeans in 1722 CE. Purported contact between Rapa Nui and South America is particularly contentious, and recent studies have reported genetic evidence for Native American admixture in present-day indigenous inhabitants of Rapa Nui [5-8]. Statistical modeling has suggested that this genetic contribution might have occurred prior to European contact [6]. Here we directly test the hypothesis that the Native American admixture of the current Rapa Nui population predates the arrival of Europeans with a paleogenomic analysis of five individual samples excavated from Ahu Nau Nau, Anakena, dating to pre- and post-European contact, respectively. Complete mitochondrial genomes and low-coverage autosomal genomes show that the analyzed individuals fall within the genetic diversity of present-day and ancient Polynesians, and we can reject the hypothesis that any of these individuals had substantial Native American ancestry. Our data thus suggest that the Native American ancestry in contemporary Easter Islanders was not present on the island prior to European contact and may thus be due to events in more recent history.