IntroductionSubmergence of graft union in grafted mango trees results in tree death, and causes loosening of the cortex in the scion. In this study, the relationship between pectin metabolism and tissue loosening, as well as the origin of the carbon dioxide release from the trunk were investigated. ResultsWhen the graft union was submerged, pectin degradation progressed only in the cortex of the scion trunk. In 2018, when the damage was severe, the amount of carbon dioxide released from the trunk was significantly high during flooded treatment throughout the experimental period. A significantly negative correlation between the pectin content in the scion trunk cortex and carbon dioxide release was observed, with the amount of carbon dioxide released increasing with decreasing pectin contents. ConclusionThese results indicate that the tissue loosening of the cortex is accompanied by the degradation of structural carbohydrate and that the increase in carbon dioxide release is caused by an increase in metabolism due to structural carbohydrate degradation.