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Cycle-cup oaks ( Quercus section Cyclobalanopsis ) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle-cup oaks remain largely unknown. Therefore, we studied this problem by conducting chloroplast genomics on 50 of the ca. 90 species. Comparative genomics and other analyses showed that Quercus section Cyclobalanopsis had a highly conserved chloroplast genome structure. Highly divergent regions, such as the ndhF and ycf1 gene regions and the petN - psbM and rpoB-trnC-GCA intergenic spacer regions, provided potential molecular markers for subsequent analysis. The chloroplast phylogenomic tree indicated that Quercus section Cyclobalanopsis was not monophyletic, which mixed with the other two sections of subgenus Cerris . The reconstruction of ancestral aera inferred that Palaeotropics was the most likely ancestral range of Quercus section Cyclobalanopsis , and then dispersed to Sino-Japan and Sino-Himalaya. Positive selection analysis showed that the photosystem genes had the lowest ω values among the seven functional gene groups. And nine protein-coding genes containing sites for positive selection: ndhA , ndhD , ndhF , ndhH , rbcL , rpl32 , accD , ycf1 , and ycf2 . This series of analyses together revealed the phylogeny, evolutionary history, and ecological adaptation mechanism of the chloroplast genome of Quercus section Cyclobalanopsis in the long river of earth history. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus ., Competing Interests: The authors declare that they have no conflict of interest. No approval/permission is required for the sample collection in accordance with relevant regulations and standards., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)