We evaluated the effectiveness of multiple types of fingerprints for representing the chemical space of natural substances. The code and data to reproduce the results are also available in the study: Boldini, D., Ballabio, D., Consonni, V., Todeschini, R., Grisoni, F., Sieber, S.A. (2024) Effectiveness of molecular fingerprints for exploring the chemical space of natural products, Journal of Cheminformatics 16, 35 (2024), https://doi.org/10.1186/s13321-024-00830-3