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Dielectric barrier discharge (DBD) air plasma is considered as a potential method for surface sterilization recently. It is a source of abundant active species, ions and charged particles. The possible induction of mutation in Candida shehatae by DBD air plasma at atmospheric pressure was verified in this study. Following the exposure of C. shehatae to DBD air plasma, two mutants (designated as C81020 and C81021) with genetic stability were isolated. Both mutants showed several protein bands in their total proteins, which differed from wild type as seen on SDS-PAGE. In addition, the ethanol productivity of the mutants decreased significantly through plasma-induced inactivation of xylose reductase and xylitol dehydrogenase. Thus, DBD air plasma was shown to have genotoxic effects on C. shehatae, and it might be used as a new method to generate mutants and with improved properties.