Present-day giant pandas ( Ailuropoda melanoleuca) are estimated to have diverged from their closest relatives, all other bears, ～20 million years ago, based on molecular data [ 1 ]. With fewer than 2,500 individuals living today [ 2 ], it is unclear how well genetic data from extant and historical giant pandas [ 3 ] reflect the past [ 3 ]. To date, there has been no complete mitochondrial DNA (mtDNA) sequenced from an ancient giant panda. Here, we use ancient DNA capture techniques [ 4 ] to sequence the complete mitochondrial genome of a ～22,000-year-old giant panda specimen (radiocarbon date of 21,910–21,495 cal BP with ± 2σ at 95.4% probability; Lab.no Beta-473743) from the Cizhutuo Cave, in Leye County, Guangxi Province, China ( Figure 1A). Its date and location in Guangxi, where no wild giant pandas live today, as well as the difficulty of DNA preservation in a hot and humid region, place it as a unique specimen to learn about ancient giant pandas from the last glacial maximum. We find that the mtDNA lineage of the Cizhutuo panda coalesced with present-day pandas ～183 thousand years ago (kya, 95% HPD, 227–144 kya), earlier than the time to the most recent common ancestor (TMRCA) of mtDNA lineages shared by present-day pandas (～72 kya, 95% HPD, 94–55 kya, Supplemental Information). Furthermore, the Cizhutuo panda possessed 18 non-synonymous mutations across six mitochondrial genes. Our results show that the Cizhutuo mtDNA lineage underwent a distinct history from that of present-day populations.