Malus fruits are covered with peel, which consists of the cuticle, epidermis and several layers of hypodermis. This peel, and especially the cuticle and epicuticular wax formed on the fruit surface, plays a crucial role in preserving the fruit life by preventing water evaporation and the penetration of pathogen, as well as maintaining fruit firmness. The protective function of these two layers is particularly important after harvest during storage. Using light and scanning electron microscopy, the present study examined the structure of the fruit peel in two apple cultivars, ‘Lobo’ and ‘Boskoop’; their fruits had been stored for 2 months in a controlled-atmosphere storehouse. The fruit epidermis in cv. ‘Lobo’, with a smooth and slick surface, was characterized by the occurrence of unidirectional microcracks that were less numerous and had a smaller depth than in cv. ‘Boskoop’. The fruit surface in ‘Boskoop’ was coarse and dry, its numerous microcracks ran in different directions along the walls of the epidermal cells. Mycelium hyphae were observed in these microcracks and inside the lenticels of the fruits of ‘Boskoop’, whereas no mycelium hyphae were found on the surface of the fruits in ‘Lobo’. The apple cultivars differed in the thickness of the cuticle layer, the height of the epidermal cells as well as in the thickness and number of hypodermis layers. Malus fruits are covered with peel, which consists of the cuticle, epidermis and several layers of hypodermis. This peel, and especially the cuticle and epicuticular wax formed on the fruit surface, plays a crucial role in preserving the fruit life by preventing water evaporation and the penetration of pathogen, as well as maintaining fruit firmness. The protective function of these two layers is particularly important after harvest during storage. Using light and scanning electron microscopy, the present study examined the structure of the fruit peel in two apple cultivars, ‘Lobo’ and ‘Boskoop’; their fruits had been stored for 2 months in a controlled-atmosphere storehouse. The fruit epidermis in cv. ‘Lobo’, with a smooth and slick surface, was characterized by the occurrence of unidirectional microcracks that were less numerous and had a smaller depth than in cv. ‘Boskoop’. The fruit surface in ‘Boskoop’ was coarse and dry, its numerous microcracks ran in different directions along the walls of the epidermal cells. Mycelium hyphae were observed in these microcracks and inside the lenticels of the fruits of ‘Boskoop’, whereas no mycelium hyphae were found on the surface of the fruits in ‘Lobo’. The apple cultivars differed in the thickness of the cuticle layer, the height of the epidermal cells as well as in the thickness and number of hypodermis layers.