A crude MeOH extract of Syzygium aromaticum (clove) exhibited preferential growth-inhibitory activity against Gram-negative anaerobic periodontal oral pathogens, including Porphyromonas gingivalis and Prevotella intermedia. By means of bioassay-directed chromatographic fractionation, eight active compounds were isolated from this extract and were identified as 5,7-dihydroxy-2-methylchromone 8-C-beta-D-glucopyranoside, biflorin, kaempferol, rhamnocitrin, myricetin, gallic acid, ellagic acid, and oleanolic acid, based on spectroscopic evidence. The antibacterial activity of these pure compounds was determined against Streptococcus mutans, Actinomyces viscosus, P. gingivalis, and P. intermedia. The flavones, kaempferol and myricetin, demonstrated potent growth-inhibitory activity against the periodontal pathogens P. gingivalis and P. intermedia.