The executive body of the Society is the Steering Committee, elected by all members of the Society for a period of five years. The present members (2015–2019) are:
- prof. RNDr. Karel Prach, CSc., prachprf [dot] jcu [dot] cz, BÚ AV ČR Třeboň, Department of Botany, University of South Bohemia České Budějovice, chairman of the Society
- doc. RNDr. Lubomír Hrouda, CSc., hroudanatur [dot] cuni [dot] cz, Department of Botany, Faculty of Science, Charles University, Praha — 1. vice-chairman
- prof. RNDr. Milan Chytrý, Ph.D., chytrysci [dot] muni [dot] cz, Department of Botany and Zoology
Faculty of Science, Masaryk University, Brno — 2. vice-chairman
- RNDr. Ivana Jongepierová, jongepierovabilekarpaty [dot] cz, Administration of Bílé Karpaty PLA - manciple
- Mgr. Michal Štefánek, stefimseznam [dot] cz, Herbarium Universitatis Carolinae Pragensis (PRC), Praha — scientific secretary
- prof. RNDr. František Krahulec, CSc.
- Ing. Jiří Danihelka, Ph.D.
- doc. RNDr. Vít Grulich, CSc.
- RNDr. Jindřich Chrtek, CSc.
- doc. RNDr. Karel Kubát, CSc.
- prof. Pavel Kovář, CSc.
- Mgr. Zdeněk Kaplan, Ph.D.
- Ing. Pavel Lustyk
- Ing. Milan Štech, Ph.D.
The supervisory body of the Society is its General Assembly, which meets annually at the occasion of the annual conference held at the end of November. All members can attend the assembly.
The Society has the following branches, sections and work groups:
- Western Bohemian Branch
- Southern Bohemian Branch
- Northern Bohemian Branch
- Eastern Bohemian Branch
- South Moravian Branch
- Moravian-Silesian Branch
- Bryo-lichenological Section
- Dendrological Section
- Floristic Section
- Work Group for Nature Protection
- Work Group for the Study of Macrophytes in Waters and Wetlands