Background <p>All species of gibbons are endangered, with the Yunnan lar gibbons (<i>Hylobates lar yunnanensis</i>) officially declared extinct in the wild in 2022. While human activities are frequently cited as major factor, the population structure, evolutionary history, and patterns of genomic erosion of endangered or extinct species remain poorly understood.</p> Results <p>We obtain genomic data from museum specimens of the extinct Yunnan lar gibbon, as well as from extant gibbon populations, and conduct a comprehensive assessment of population history and the genomic consequences of recent declines. Our findings indicate that Pleistocene climate change greatly impacted the available habitats of the lar gibbon. In addition to climatic factors, we observe a bimodal distribution of heterozygosity in the Yunnan lar gibbon, likely resulting from a severe recent inbreeding event following a population bottleneck, which pushed the population to the brink of collapse. By integrating genomic data from other gibbon species, we propose that the heterozygosity distribution serves as a better indicator for assessing the conservation status of gibbon species.</p> Conclusions <p>The interaction between genomic features and external factors, such as environmental conditions, likely contributed to the extinction of the Yunnan lar gibbon. The insights and resources generated from this study will boost the research in gibbon conservation genomics and assist in determining conservation priorities, evaluating, and improving conservation measures.</p>