Since cold atmospheric pressure plasma (CAP) has not only bactericidal activity but also fungicidal activity without toxic residues and thermal damage, it is considered as an alternative method for sterilization of fungi on the surfaces of perishable foodstuffs and human bodies. Aureobasidium pullulans is a ubiquitous yeast-like fungus and called black yeast because it produces melanin, a dark biological pigment. It is well known that various melanized fungi show hyper-resistance to extreme stress conditions including high levels of radioactivity. Curiously, however, there is very little information about the fungicidal effects of CAP on melanized fungi. Therefore, we herein investigated the effects of CAP on A. pullulans, using cold atmospheric argon plasma (Ar plasma). We found that ammonium sulfate repressed the synthesis of melanin in A. pullulans as well as Aureobasidium melanogenum. Although the non-melanized A. pullulans cells were efficiently killed by the exposure of Ar plasma, the melanized cells showed the significant resistance to Ar plasma as well as to hydrogen peroxide and thermal stress. In order to improve the fungicidal efficacy of Ar plasma, we examined the combination of Ar plasma and Fenton reaction. We realized that FeCl2 and FeSO4 significantly improved the sterilization efficacy of Ar plasma on the melanized A. pullulans.