Paddy field is an important source of methane emission to atmosphere. Bioturbation activities of aquatic earthworms in paddy soil add oxygen in lower soil layers by pumping oxygen rich water to those layers. Thus it was hypothesized that aquatic earthworm’s activities may accelerate oxidation of methane in paddy field. Therefore a factorial design (2×2) experiment was conducted during May-October, 2011 to determine the role of aquatic earthworms on methane emission from paddy field under different farming practices. Two levels of tillage (no-tillage and tillage) and two different fertilizers (chemical and organic) were imposed with four replications. Organic fertilizer had marginal significant effect on earthworm density. The highest earthworm density was found in no-tillage plot with organic fertilizer, whereas the lowest earthworm abundance was observed in same plot with chemical fertilizer. The effect of earthworms on methane flux was found temporally context-dependent. In August, decreasing trend of methane flux was observed in the plots with high earthworm abundance. However, opposite trend was noticed during succeeding month. The study results revealed that proper farming practice may influence favorable environment for aquatic earthworm’s activity that might contribute in methane mitigation in paddy field ecosystem.