From the previous findings, the ethanolic fractionated extract of Caesalpinia sappan (F-EtOH) has high activity against Streptococcus mutans, the most severe cariogenic bacteria. The present study was aimed to isolate and identify the active compound of F-EtOH and compare its inhibitory activity against the biofilm of S. mutans as well as the cytotoxicity to oral fibroblast cells with F-EtOH. Compound isolation was done by column chromatography. The active compound was identified using liquid chromatography-mass spectrometry with electrospray ionization and nuclear magnetic resonance spectroscopy. It was found that the major compound of F-EtOH is brazilin. F-EtOH and brazilin were compared for inhibitory potential on the biofilms of three strains of S. mutans. The results exhibited that both F-EtOH and brazilin had potential on inhibiting biofilm formation and eradicating the preformed biofilms and their activity was dose dependent. F-EtOH showed significantly less toxic to normal periodontal ligament fibroblast than brazilin. At low concentration of 1- and 2-MBC, F-EtOH showed higher effective than brazilin. The results of our study suggest that the antibacterial activity of F-EtOH is according to the synergistic effects of the existing compounds including brazilin in F-EtOH.