Fouling organisms cause serious problems by settling on ships’ hulls, and other marine infrastructures. Organotin compounds have been developed as effective antifoulants. However, environmental problems are associated with these compounds. It is necessary to find antifouling substances that exhibit a lower toxicity than those substances currently used. A new pyrimidine derivative, 3,4,5,6‐tetrahydro‐6‐hydroxymethyl‐3,6‐dimethyl‐4‐pyrimidinecarboxylic acid, (compound 1) and zooanemonin (compound 2) were isolated from the marine sponge Protophlitaspongia aga as antifouling substances against the barnacle Balanus amphitrite. We also found that α‐nicotinamide ribose (compound 3) inhibited germination and the attachment of Ulva spores.