| Summary: | <i>Ginkgo biloba</i> has unique leaf color and high ornamental value. Here, we conducted seasonal dynamic analyses of leaf color, morphology, physiology, and biochemistry in the new variety Huangjinwanliang (HJWL), using the golden-leaf ginkgo Xiajin (XJ) as a control, and performed genotyping-by-sequencing (GBS) to explore genetic differences. The results showed that both varieties were golden-yellow leaves in spring and autumn, transitioning to green in summer. The total chlorophyll and carotenoid contents in HJWL (1.45~4.84 mg/g and 0.09~0.39 mg/g) were significantly higher than those in XJ (1.42~3.93 mg/g and 0.08~0.34 mg/g). HJWL exhibited a higher number of chloroplasts, with visible single lamellar thylakoids, whereas XJ had fewer chloroplasts. Chloroplast fluorescence and photosynthetic parameters indicated that HJWL possesses a greater capacity for light acclimatization. The total flavonoids and wax content of HJWL (16.67 ± 0.33 mg/g and 18.22 ± 0.15 mg/g) were significantly higher than those of XJ (14.15 ± 0.31 mg/g and 30.19 ± 0.18 mg/g). GBS analysis revealed distinct genome-wide molecular bases between HJWL and XJ. These findings demonstrate that HJWL’s leaf color and extended ornamental period make it a valuable landscape tree species for spring and autumn, suitable for promotion as an ornamental tree.
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