Water stress problems including drought stress and flooding are the most important factors limiting in citrus growth, development and production. The main purpose of this study was to investigate the effects of putrescine on reducing negative effect of flooding of Carrizo Citrange (Citrus sinensis Osb. × Poncirus trifoliata Raf.) and Volkameriana (Citrus volkameriana) rootstocks under flooding condition. Three concentrations of putrescine [0.0, 1.0 and 2.0% (w/v)] were sprayed on all the leaves of two mentioned rootstocks in a factorial experiment in a completely randomized design under flooding and field capacity conditions. In comparison to the field capacity condition, growth vegetative indicators, RWC, SPAD unit, stomatal conductance (gs), chlorophyll a and b content, chlorophyll fluorescence yield (Fv/Fm), and CO2 assimilation rate (AcO2) decreased in the flooded seedlings whereas intercellular CO2 concentration (Ci), SOD, and CAT antioxidant enzymes activities increased. Putrescine foliar application particularly in 2 mM concentration, resulted in a decrease in the intercellular CO2 concentration and an increase in the other study values. Overall, putrescine could help seedlings against flooding stress through increasing growth, improving physiological statuses, and reducing oxidative damages.