Acta Phytotaxonomica Sinica is sponsored by the Botanical Society of China and the Institute of Botany, Chinese Academy of Sciences. It was founded in 1951, continuing publications of the four Chinese botanical journals before 1949, viz., Bulletin of the Fan Memorial Institute of Biology, Botanical Series; Contributions from the Institute of Botany, National Academy of Peiping; Botanical Bulletin of Academia Sinica; and Contributions from the Biological Laboratory of the Science Society of China, Botanical Series.

Starting from 2008, the English title changed to Journal of Systematics and Evolution.