The Botanical Society of Japan Awards, established in 2004, commend botanical achievements. They consist of the following:
- The "BSJ Fundamental Prize" is awarded to a botanist who has contributed to BSJ and to the development of plant sciences.
- The "BSJ Academic Prize" is awarded to a botanist who has undertaken highly original studies and whose academic publications have been admired internationally.
- The "BSJ Encouragement Prize" and "BSJ Young Botanist Prize" are awarded, respectively, to researchers and young botanists who have demonstrated research excellence.
- The "BSJ Special Prize" is awarded to researchers who contribute to the development of plant sciences in areas such as research techniques, scientific outreach and education, and other affiliated fields.
- The "Journal of Plant Research Best Paper Award" is awarded to botanists who have contributed a highly original article to JPR that has significantly advanced plant sciences.