Abstract
In the current research, we focus on uniparental inheritance of chloroplast genome of the living fossil plant, Ginkgo biloba L., one of the gymnosperms, using genomic data.•Our results provide strong genomic evidence to support plastid maternal inheritance mode of G. biloba, which is different from most other gymnosperms.•The combination of manually genetic crosses and genomic data is proved to be an efficient way to investigate the inheritance mode of chloroplasts genome in land plants.•The current research also provides a case study for further research of plastid inheritance in gymnosperms using genomic techniques, which will contribute to a better understanding of cytologically uniparental inheritance mode and evolutionary mechanism of plastids in both gymnosperms and angiosperms.