The fruit cracking in pomegranate is an important physiological disorder limiting its fruit quality as well as yield potential. In the present study, fruit cracking behaviour in five pomegranate varieties namely, Bhagwa, Mridula, Kandhari, Jodhpur Red and Ganesh was evaluated in relation to changes in peel thickness, peel moisture, antioxidants, phenols and anthocyanin. Pomegranate variety Kandhari, which registered no cracking, contained the highest level of total phenols, antioxidants and anthocyanin content, while the variety Jodhpur Red recorded minimum content of these phytochemicals and the maximum cracking. Further, the activity of the cell wall degrading enzymes viz., polygalacturonase and cellulase were the highest in the peel of variety exhibiting maximum cracking i.e., Jodhpur Red. Scanning electron microscopy (SEM) analysis of cracked and healthy peels of Jodhpur Red and Kandhari varieties demonstrated isodiametric, well organized cells with no intercellular spaces that possibly impart crack resistance to Kandhari variety whereas, transversely elongated and disorganized cells with intercellular spaces render Jodhpur Red susceptible to cracking.