The seasonal courses of methane (CH4) and nitrous oxide (N2O) fluxes were simultaneously monitored in a paddy field using a closed chamber system with automated gas sampling and analyzing equipment. Water management and fertilizer application practices followed Japanese conventional ones. CH4 flux gradually increased after the first flood irrigation of the field and reached ∼150 mg CH4 m−2 d−1 at the beginning of July. After the first summer drainage, however, CH4 flux dropped rapidly to almost zero within a few days. CH4 flux then gradually increased again according to intermittent flood irrigations, but was much less than that before the first drainage. Immediately after the first flood irrigation, N2O flux rapidly increased, although its temporal peak lasted only within a few days. During the subsequent continuously and intermittently flooded periods, N2O flux remained at almost zero until the final drainage, except for slight and temporal peaks just after the top-dress application of supplemental fertilizer. About 1 week after the final drainage in autumn, N2O flux gradually increased, and the most significant high peak of N2O flux was observed after the harvest of rice plants, which lasted for about 2 weeks. The amounts of cumulative CH4 and N2O emissions throughout the whole year of 2002 were 3128 mg CH4 m−2 and 60.2 mg N m−2, respectively. Both the amounts of cumulative CH4 and N2O emissions during the rice cultivation period were low compared with those reported in previous studies. These results suggest the advantage of Japanese conventional water management and fertilizer application for reducing the combined effect for global warming by CH4 and N2O emissions from paddy fields, since the practices of drainage and intermittent flood irrigation in summer markedly lessen CH4 emission in the latter half of the rice cultivation period with little enhancement of N2O emission.