In this study, the expression of genes related to fruit ripening was investigated using realtime PCR. The study aimed to determine the effective conditions of calcium compounds (Calcium citrate, calcium chloride, calcium nitrate, GH-Ca, OS-Ca) and chitosan treatment to extend the shelf-life in the ‘Kumhong’ nectarine and ‘Madoka’ peach fruits. In this study, in the ‘Kumhong’ and ‘Madoka’ fruits, the expression of genes related to cell wall degradation, pectin lyase (PL), polygalacturonase (PG), and pectin methylesterase (PME), was inhibited by calcium, chitosan, or a mixture (Chitosan+CaCl2) treatment. In ‘Madoka’ peach, although the expression of the PG gene was suppressed at pre-harvest Ca and chitosan treatment, the expression of the PL gene was induced at pre- and post-harvest Ca and chitosan treatment compared to the control. The spray of calcium, chitosan itself, or a mixture (Chitosan+ CaCl2) on the trees at the ripening stage and harvested fruits can extend the shelf-life by suppressing the expression of cell wall degrading enzymes genes (PL, PG, PME) in ‘Kumhong’ nectarine and ‘Madoka’ peach tree. These results provide valuable information for the development of technology for the extension of the shelf-life of peach and nectarine fruits.