Lowest seed yield was recorded in both the varieties (T21 and Bahar) of pigeonpea, in pot culture, due to waterlogging at post flowering, followed by waterlogging at flowering stage during both the years. A significant Interaction between varieties and waterlogging has been observed during 1991 for seed yield. Waterlogging (nine days). adversely affected the nitrogen content in seed and yield of pigeonpea genotypes than waterlogging of three days during both the years. Bahar has been identified as tolerant variety under waterlogged conditions.