Antifouling agents with low toxicity are in high demand for sustaining marine industries and the environment. This study aimed to synthesize 15 isothiocyanates derived from β‐citronellol and evaluate their antifouling activities and toxicities against cypris larvae of the barnacle Amphibalanus amphitrite. The synthesized isothiocyanates exhibited effective antifouling activities (EC50=0.10–3.33 μg mL−1) with high therapeutic ratios (LC50/EC50 >30). Four isothiocyanates with an amide or isocyano group showed great potential as effective antifouling agents (EC50=0.10–0.32 μg mL−1, LC50/EC50=104–833). The enantiomers of the isothiocyanates only slightly differed in their antifouling activities. These results may serve as a basis for further research and development of β‐citronellol‐derived isothiocyanates as effective low‐toxic antifouling agents. To the best of our knowledge, this study is the first to report the antifouling activities of isothiocyanates derived from accessible natural products.

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