Two compounds, 2-hydroxymyristic acid (HMA) and cis-9-oleic acid (COA), were isolated from a chloroform extract of the marine bacterium, Shewanella oneidensis SCH0402. In a spectrophotometer-based chemotaxis assay, HMA completely eliminated the optical density (OD) of Alteromonas marina SCH0401 and Bacillus atrophaeus SCH0408, motile, fouling bacteria, at 100 and 1000 μg ml−1, respectively. COA similarly decreased the OD of A. marina and B. atrophaeus by 100% at 1000 μg ml−1. The commercially available, highly toxic anti-fouling compound, tributyltin oxide (TBTO) never reduced the OD of the target bacteria by 100% even at higher concentration. Instead, all the test bacterial cells were killed at higher than 1000 μg ml−1 of concentration. Both HMA and COA inhibited germination of Ulva pertusa spores completely at 10 and 100 μg ml−1, respectively, while TBTO inhibited germination at 0.01 μg ml−1. However, in field assays, both HMA and COA showed anti-fouling activities as potent as TBTO against a wide range of fouling organisms, including micro- and macro-algae, barnacles, and mussels. The average fouling coverage on the surface of the control panel was 93 ± 6% after 1.5 years but no fouling was observed on the surface of the test panel onto which each compound was applied separately. Thus, bacterial repellent compounds can be used as substitutes for potent toxic anti-fouling compounds, resulting in higher standards of environmental safety without loss of anti-fouling performance.