We investigated eight active natural antimicrobials for preservation of functional beverages that are usually degraded by yeasts rather than by bacteria due to a high sugar content and a low pH. Five strains of yeasts (S. cerevisiae, Z. bailii, P. membranaefaciens, C. albicans, and P. Anomala) were tested with eight natural antimicrobial agents (ε-polylysine, yucca extract, vitamin B1 derivative, scutellaria baicalensis extract, chitooligosaccharid, allyl isothiocyanate, sucrose-fatty acid ester, and oligosaccharide). The lowest minimal inhibitory concentrations (MIC) were 10 ppm for oligosaccharide and sucrose-fatty acid ester against S. cerevisiae and Z. bailii, 10 ppm for allyl isothiocynate against P. membranaefaciens and C. albican, and 10 ppm for allyl isothiocynate and oligosaccharide against P. anomala . No growth were observed for five kinds of yeasts in functional beverages containing sodium benzonate at concentration of 0.015% or higher. The resistance of S. cerevisiae, Z. bailii, and P. Anomala against natural antimicrobial agents was lower than those of P. membranaefaciens and C. albican. Allyl isothiocyanate, oligosaccharide, and sucrose- fatty acid ester showed the highest antimicrobial activities among the eight tested antimicrobials. These results can be applied to develop new natural antimicrobial agents to improve microbial quality of functional beverages.