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Historically, the giant panda was widely distributed from northern China to southwestern Asia [ 1 ]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [ 2 ]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions. • First nuclear paleogenome of the giant panda • Represents a population that forms the sister group to all extant populations • Differential admixture between extinct and extant panda populations • Part of the extinct, ancient population survives in the modern gene pool Sheng et al. present the first nuclear paleogenome of the giant panda, one of the most iconic mammalian species. Their results elucidate the population history of this species during the Holocene and show that although some genetic diversity was lost, parts of the genome of extinct populations survive in the extant panda gene pool. [ABSTRACT FROM AUTHOR]