Tobacco is an agricultural crops of high economic value. The uncertain climate caused farmers is difficult to predict the coming of the rain, so that tobacco farming is often hit by waterlogging and flooding. Waterlogging of harvest failure. Therefore, it is necessary to investigate the influence of waterlogging stress in tobacco plants. Research also has the benefit of getting tolerant varieties waterlogging stress. The parameters observed plant height, root length, number of adventitious roots, dry weight, the ratio of roots and canopy observation aerenchyma area. Data were analyzed using Two-way ANOVA followed by Tukey's test, with a level of 95%. The results showed that the interaction between varieties and treatments waterlogging stress affects the parameters of root length, plant height, number of adventitious roots and dry weight of plants. The results showed that the waterlogging stress cause deterioration in growth, adventitious root formation and aerenchyma in plants. Tolerant varieties Sensitivity Index is based on the calculation of varieties Paiton 1 and Maesan 1.