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Background Styrax , a vital raw material for shipbuilding, construction, perfumes, and drugs, represents the largest and most diverse genus in the Styracaceae. However, there is a relative scarcity of research on Styrax , particularly in evolution and genetics. Therefore, this study conducted comparative and evolutionary analyses of the chloroplast genomes of five rare Styrax species ( S. argentifolius , S. buchananii , S. chrysocarpus , S. finlaysonianus , and S. rhytidocarpus ). Results The results indicated that, despite high levels of conservation in chloroplast genome structure among these species, specific mutation hotspot regions exist, particularly involving the expansion and contraction of the IR region. Additionally, evidence of positive selection was detected in eight genes ( atpB , ccsA , ndhD , petA , rbcL , rpoC1 , ycf1 , and ycf2 ), which may be associated with adaptive evolution in response to environmental changes. Phylogenetic analysis revealed conflicts between trees constructed based on coding sequences and complete chloroplast genomes for several species, which were similar to previous phylogenetic studies. Conclusion This study underscores the importance of increasing sample sizes to enhance the accuracy of phylogenetic analyses and provides a new perspective on understanding the adaptive evolution of Styrax species. These findings are not only important for the conservation and sustainable use of Styrax , but also provide valuable insights for research in plant evolution and ecology within the genus.