Yam has been recognized as healthy food due to its various biological activities, such as anti-obesity, antimicrobial, anticancer and immune-stimulation activities. In this study, antibacterial activities of 800 more natural plant extracts against yam-putrefactive psychrotrophic bacterium, Pseudomonas rhodesiae YAM-12, were evaluated to select a natural preservative, which is useful to long-term storage of yam and fresh-cut production. Finally, the clove oil was selected, and applied for the production of yam fresh-cut. The 1% of clove oil treated fresh-cut showed minor color changes during 31 days storage at $4^{circ}C$ and the microbial growth was not detected. When the artificially contaminated fresh cut by dipping with P. rhodesiae YAM-12 suspension for 3 min was treated 1% clove oil, the microbial growth was identified to $10^4$ CFU/g from $10^3$ CFU/g with minor color changes. Whereas, treatment of sterilized water, or 100 ppm NaOCl into artificially contaminated fresh cut showed severe putrefaction $(10^8;CFU/g)$ and color changes. Considering the previous reports that clove oil has antimicrobial, antioxidation, and antithrombosis activity, the use of clove oil into the yam fresh cut will provide market safety and consumer acceptability by prevention of microbial putrefaction and its biological activity.