Objective Waterlogging is one of the main obstacles affecting the growth of black sesame.Identification of waterlogging tolerance of black sesame germplasm resources at seedling stage and screen reliable evaluation indexes can provide theoretical basis for breeding and cultivation of waterlogging-tolerant black sesame varieties. Method 52 black sesame germplasm resources were selected as experimental materials and they were waterlogged for 7 days at seedling stage.Seven indexes，including seedling survival rate，plant height and root length，were measured，and the waterlogging tolerance coefficient of each index was calculated.Principal component analysis，membership function analysis，cluster analysis，correlation analysis and stepwise regression analysis were used to comprehensively evaluate the waterlogging tolerance of different black sesame germplasm resources and screen the waterlogging tolerance indexes. Result Seven indicators were simplified into four independent comprehensive indicators by principal component analysis，which contained 79.25% of all information；Based on the comprehensive evaluation results of waterlogging tolerance and the classification of waterlogging tolerance grades，five varieties with high waterlogging tolerance，39 varieties with moderate waterlogging tolerance and eight varieties with waterlogging sensitivity were screened out.Correlation analysis showed that plant height，root length，aboveground biomass and underground biomass were the main influencing factors of comprehensive evaluation value，and there were also different degrees of correlation among all indexes.Four key indexes such as plant height，root length，aboveground biomass and underground biomass，were screened out from seven identification indexes by regression analysis. Conclusion Based on the above analysis，Poyang black sesame，Xingzi black sesame，Duoshuo black sesame，Duchang black sesame and 17-50 were the most waterlogging tolerant and can be used as excellent parents for breeding；The plant height，root length，aboveground biomass and underground biomass are critical indexes to rapidly identify the waterlogging-tolerance of sesame seedlings.