A heterotrophic marine bacterium Bacillus amyloliquefaciens isolated from seaweed Padina gymnospora exhibited broad spectra of antibacterial activities against pathogenic bacteria Aeromonas hydrophila, Vibrio harveyi, Vibrio vulnificus, and Vibrio parahaemolyticus. The seaweed-associated B. amyloliquefaciens was recognized to possess functional type I polyketide synthase-1 (pks-1) gene, and was used to isolate four homologous compounds with polyketide frameworks. The compounds were characterized as 11-(15-butyl-13-ethyl-tetrahydro-12-oxo-2H-pyran-13-yl) propyl-2-methylbenzoate (1), 9-(tetrahydro-12-isopropyl-11-oxofuran-10-yl)-ethyl-4-ethoxy-2-hydroxybenzoate (2), 12-(aminomethyl)-11-hydroxyhexanyl-10-phenylpropanoate (3), and 7-(14-hydroxypropan-13-yl)-8-isobutyl-7,8-dihydrobenzo[c]oxepin-1(3H)-one (4) by comprehensive nuclear magnetic resonance and mass spectroscopic experiments. The compounds 1-4 displayed significant antibacterial activities against clinically important pathogens V. parahaemolyticus and V. vulnificus (inhibitory zone diameter of ≥15 mm, 100 mcg on disk). The electronic and hydrophobic parameters appeared to hold a conspicuous part in directing the antibacterial properties of the compounds. This study revealed seaweed-associated B. amyloliquefaciens as potential source of antimicrobial polyketides for pharmaceutical applications.