This study carried out development of a natural antimicrobial agent from Schima wallichii ssp. liukiuensis. Compound I exhibiting potent antimicrobial activity against Candida spp. was isolated from the methanol extracts of Schima wallichii ssp. liukiuensis. The structure of I identified as a sterol glycoside consisted of a trisaccharide and α1-sitosterol. Trisaccharide composed of L-rhamnose, D-galactose and D-glucose residues. The antimicrobial activity of I was selective on yeast rather than bacteria or other fungi. Compound I was demonstrated to be ineffective against toxicity to mouse liver cells where as protective to human dermal fibroblast cells at low concentrations. Thus, it is reasonable to expect a sterol glycoside (I) as a valuable alternative for synthetic antifungal.