Candida albicans is an opportunistic human pathogen whose disinfection is a challenge. ε-Poly-L-lysine (ε-PL), an antagonistic agent, can disrupt cell membranes and inhibit the growth of C. albicans. Genes that were differentially-expressed in response to ε-PL were isolated from C. albicans and identified by suppression subtractive hybridization. Ten subtracted clones, that share >98 % homology with known genes of C. albicans, were isolated. Among these, four genes encoded cell wall-associated proteins. Real-time quantitative PCR and northern blot hybridization suggest that these genes are involved in the response to ε-PL. These findings will help to determine the mechanism of the antimicrobial activity of ε-PL against C. albicans.