In the present study, eight natural products that belonged to di(1H-indol-3-yl)methane (DIM) family were isolated from Pseudovibrio denitrificans UST4-50 and tested for their antifouling activity against larval settlement (including both attachment and metamorphosis) of the barnacle Balanus (=Amphibalanus) amphitrite and the bryozoan Bugula neritina. All diindol-3-ylmethanes (DIMs) showed moderate to strong inhibitory effects against larval settlement of B. amphitrite with EC50 values ranging from 18.57 to 1.86 μM and could be considered as low-toxicity antifouling compounds since their LC50/EC50 ratios were larger than 15. Furthermore, the DIM- and 4-(di(1H-indol-3-yl)methyl)phenol (DIM-Ph-4-OH)-treated larvae completed normal settlement when they were transferred to clean seawater after being exposed to those compounds for 24 h. DIM also showed comparable antifouling performance to the commercial antifouling biocide Sea-Nine 211(™) in the field test over a period of 5 months, which further confirmed that DIMs can be considered as promising candidates of environmentally friendly antifouling compounds.