During the Fusetani Biofouling Project, isolation of natural products from benthic organisms was carried out in an attempt to develop nontoxic antifouling agents. In fact, more than 50 compounds showing antifouling activity against barnacle larvae have been obtained from marine invertebrates. 3-Isocyanotheonellin, isolated from a nudibranch species, exhibits potent antifouling activity against the larvae of the barnacle Balanus amphitrite (EC₅₀ 0.13 µg/mL). However, its toxicity at high concentrations and structure–antifouling activity relationship have not yet been demonstrated. Herein, the structure–antifouling activity relationship studies conducted by synthesizing 3-isocyanotheonellin and its analogues are described. Based on these studies, various antifouling active isocyano compounds have been designed for developing environmentally friendly antifouling agents. In this review, the antifouling activity of isocyanides derived from citronellol and amino acids is mainly described. Most of these compounds showed potent antifouling activity without any significant toxicity against the cyprid larvae of the barnacle. These results suggested that isocyano compounds could be developed as environmentally friendly antifoulants in the near future. In addition, attempts to elucidate the mechanism underlying the expression of antifouling activity for the isocyano compounds are described.