Abstract: 【Objective】The objective of this study was to investigate the effects of waterlogging on physiological response and waterlogging tolerance of moringa seedlings, provide reference for the breeding of waterlogging-tolerant cultivars and the study for waterlogging-tolerant cultivation mechanism of moringa.【Method】Moringa oleifera Lam., PKM1(a variety of M. oleifera) and Moringa stenopetala(Baker f.) Cufod. were used as experimental materials. Experimental treatments consisted of no waterlogging(CK) and waterlogging. The experiment was performed to explore the effects of waterlogging on soluble sugar(SS), soluble protein(SP), proline(Pro), chlorophyll a(Chl a), chlorophyll b(Chl b), carotenoid(Car), chlorophyll a/b(Chl a/b), chlorophyll a+b(Chl a+b), total chlorophyll(Chl T), minimal fluorescence(F_o), maximum fluorescence(F_m), photochemical efficiency of photosystemⅡ(PSⅡ) (F_v/F_m), actual photochemical efficiency of PSⅡ(ΦPSII), electron transportation rate(ETR), non-photochemical quenching coefficient(NPQ) and photochemical quenching coefficient(qP) of moringa, and to evaluate the waterlogging tolerance of M. oleifera, PKM1 and M. stenopetala.【Result】Results showed that SS, SP and Pro of PKM1 and M. stenopetala were significantly increased by 38.64%, 86.81%, 351.07% and 69.66%, 139.22%, 567.69%, respectively, compared to CK(P<0.05, the same below). SS of M. oleifera was significantly increased by 29.12% compared to CK, but SP was significantly decreased by 55.35%. Chl b of M. oleifera was significantly decreased by 36.59% compared to CK, and Car of M. stenopetala was significantly increased by 57.14%. Chl a/b of M. oleifera, PKM1 and M. stenopetala were significantly increased by 36.41%, 38.92% and 26.34%, respectively, compared to CK. F_o of M. oleifera, PKM1 and M. stenopetala were significantly increased after waterlogging compared to CK. F_v/F_m, ΦPSII, ETR and qP of all experimental materials were significantly decreased after waterlogging compared to CK, and NPQ was not significantly different from CK(P>0.05). F_m of PKM1 and M. stenopetala were significantly decreased by 37.79% and 34.90%, respectively, compared to CK. The fast light response curves showed that, the ETR_max of M. oleifera, PKM1 and M. stenopetala were decreased after waterlogging. ETR_max rank after waterlogging was M. stenopetala > PKM1 > M. oleifera. By using multivariate analysis methods such as principal component analysis, membership function method and cluster analysis, the comprehensive analysis of 16 single indexes showed that the waterlogging resistance ranked as M. stenopetala > PKM1 > M. oleifera.【Conclusions】Waterlogging increases osmotic adjustment substances of moringa seedlings, and seriously affects photosynthetic and chlorophyll fluorescence characteristics. Therefore, the prevention and control of waterlogging should be strengthened at the seedling stage of moringa, and the water should be drained in time. Waterlogging-tolerant varieties should be selected in the area where waterlogging occurs frequently.