The Journal of Japanese Botany was started by Tomitaro Makino in April 1916. He edited the Journal through vol. 8 in 1933. Subsequently, the Journal has been edited by The Editorial Board of The Journal of Japanese Botany from vol. 9 no. 1 in May 1933 to the present issue. The Editorial Board has been represented by Yasuhiko Asahina (1933–1975), Hiroshi Hara (1975–1987), Shoji Shibata (1987-2006), and Hiroyoshi Ohashi (2006–present) as the Editor-in-Chief. The Journal is now published by Tsumura & Co. It has promoted the development of research and the study of systematic botany, pharmacognosy and related disciplines. It is among the highly regarded journals in its field.
We published "Centennial Memorial Issue" as Vol. 91 Supplement, December 2016. To mark our centenary, we, The Editorial Board of The Journal, released also digital archives of the journal to make both viewing and searching its contents easier. In 2023, our digital archives are transferred to J-STAGE platform. We hope that the journal could contribute more extensively to the efforts of researchers in botany and pharmacognosy worldwide and allow an even larger readership easier access to the resources that the journal offers.
Papers published within current two years will be released only for personal subscribers of the journal and other papers published three years before are free.

Private addresses of the authors printed in the journal are deleted in the digital archives.

New names in science and Japanese and new typifications published in each issue are shown in the last page(s) since volume 94 number 2 (2019). Previously, the new scientific and Japanese names were listed on the second page of each issue after volume 74 (1999).