To study the effect of weed control methods on weed seed bank and composition of weed flora in wheat and rice under wheat-rice system, a field experiment was conducted at crop research center of GBPUAT, Pantnagar during rabi and kharif of 2001-02 and 2002-2003. The weed seed bank studies revealed that application of herbicides has no significant effect on the weed seed bank of soil. Weed control treatments isoproturon + hand weeding in wheat and butachlor + hand weeding in rice recorded less number of weed seeds (14450, 3800 and 605 of Phalaris minor, Chenopodium album and Melilotus alba, respectively in wheat and 2650, 2048 and 4265 of Echinochloa colona, Echinochloa crusgalli and Paspalum scrobiculatum, respectively in rice). Under the influence of different weed management practices, there was significant negative relationship of grain yield with weed dry weight and weed seed bank in both wheat and rice. Among herbicide treatments, isoproturon (1.0 kg/ha) + hand weeding; butachlor (1.5 kg/ha) + hand weeding followed by isoproturon (1.0 kg/ha) +2,4-D (0.5 kg/ha); butachlor (1.5 kg/ha) fb 2,4-D (0.5 kg/ha) + organic matter through Sesbania aculeata were found effective in reducing total weed population, weed dry matter and weed seed density there by increasing yield of wheat and rice.