•Fruit cracking is a major physiological disorder of lemon and lime.•Light microscopy and scanning electron microscopy of healthy and cracked peel and pedicel was performed.•The cracked fruit peels were coarser and thinner with empty oil glands as compared to healthy cracked fruit peel.•The xylem of cracked fruit pedicel was disorganized resulting in disruption of water and mineral flow to the fruit causing cracking. Fruit cracking is a major physiological disorder of lemon and limits the productivity of this fruit. The present study was conducted to compare the structural variation in peel and pedicel of healthy and cracked fruits of lemon. Sections of healthy and cracked fruit peel, stem end and pedicel were analyzed by light microscope and scanning electron microscopy (SEM). The ultra-structure of peel of healthy and cracked lemons showed significant difference in peel thickness, epidermal thickness, arrangement of oil glands and vascular tissues. The pedicel of cracked fruit exhibited collapsed and deformed xylem tissues. Ruptured oil gland pits, rough surface and reduced peel thickness was observed through SEM in cracked fruits as compared to healthy fruits. The coarse thinner peels with smaller epidermal thickness and larger empty oil glands are prone to fruit cracking as compared to smooth peels of healthy fruits. The xylem tissue in cracked fruit pedicel was disorganized that disrupts the water and mineral flow to the growing fruit. The disorganization of xylem tissue may be due to irregularity in water transport followed by pulp expanding resulting in thinner peels leading to fruit cracking. New It is a new finding that fruit cracking in lemon is possibly due to irregularity in influx of water that creates tension in xylem vessels. This results in disorganization of vascular tissues of pedicel, which disrupts the regular transport of water and nutrient to developing albedo and flavedo and cause fruit cracking.