Actinidin is a major protein contained in kiwifruit (Actinidia spp.). While uptake of actinidin is beneficial to help gastric protein digestion with cysteine protease activity, the protein is also recognized as a major elicitor of allergy which can induce tingling in the oral cavity and occasionally severe anaphylactic reactions. Given that consumption of fresh kiwifruit has increased globally, development of Actinidia cultivars with lower level of actinidin is required to reduce the risk of allergenicity. In the present study, we examined variations in the actinidin level in Actinidia varieties. Among several varieties having trace amounts of actinidin, A. chinensis 'Kohi' was targeted to be analyzed for the molecular basis for the phenotype. 'Kohi' had below the detectable transcript level of Act1a, a critical gene for actinidin level. The upstream region of Act1a in 'Kohi' constituted different sequences from that of A. deliciosa 'Hayward', which has an active promoter for high expression of Act1a. The 'Kohi' sequence in the diverged region (upstream from −873 b) was rich in cytosine residues methylated at a higher level than in 'Hayward'. Our data suggest the possibility of novel epigenetic regulation to reduce the actinidin level. The molecular mechanism for the phenotype in 'Kohi' was differentiated from 'Hort16A', a globally popular cultivar with a low level of actinidin. This cultivar could be a choice as a genetic resource in breeding to develop cultivars with controlled actinidin levels.