Sixty-six sesame germplasm were treated by waterlogging at the full flowering stage, and the results were showed that there were obvious difference in yield characteristics of monaxial and ramification sesame germplasm. The waterlogging index of seed weight per plant (69.18％) >capsules per plant (67.48％) > capsule nodes per plant (49.10％) >length of capsule axis (45.69％) > height per plant (16.40％) in monaxial germplasm and that of branch capsule nodes per plant (65.96％) > branch capsules per plant (64.73％) > total of capsules (52.01％) > seed weight per plant (49.92％) > main axis capsules per plant (41.66％)> length of main axis capsule axis per plant (37.57％) > branches per plant (34.21％) > main axis capsule nodes per plant (20.12％) > height per plant (15.43％) in ramification germplasm. Monaxial tricapsular germplasm treated by waterlogging showed waterlogging index of numbers of side capsule (92.25％) > numbers of middle capsule (50.25％), and ramification tricapsular germplasm with waterlogging showed waterlogging index of numbers of branch side capsule per plant (92.86％) > numbers of main axis side capsule per plant (69.14％) > numbers of branch middle capsule per plant (44.17％) > numbers of main axis middle capsule per plant (32.97％). According to clustering analysis on relative yield after waterlogging, these germplasm could be classified into waterlogging tolerance and non waterlogging tolerance type, 61 germplasm belonged to non waterlogging tolerance type, accounting for 92.42％, the other 5 germplasm with waterlogging tolerance were worth to be utilized, which were Zhushan Baizhima, Xiping Erlanghua, Funan Zhima, Jiaxing Jinkouhei and Macheng Heizhima, respectively, with the ratio of 7.58％.