A randomized field experiment with three replicates was conducted in the subtropical region of China to investigate the effects of integrated riceduck system (RD) on methane (CH 4 ) emission, active soil organic carbon fractions and their relationships in 2007 and 2008, compared with conventional rice system (CK). Methane emissions were measured at 7-9 days intervals using a closed static chamber technique, and two fractions of active soil organic carbon, namely, dissolved organic carbon (DOC) and microbial biomass carbon (MBC), were analyzed simultaneously. Soil DOC and MBC in RD and CK had similarly distinct seasonal variation patterns within the 2 years. During this time DOC and MBC concentrations were low at the early growth stage, increased during panicle differentiation and heading period, and dropped during grain filling period of rice. CH 4 emission fluxes from RD and CK followed a similar seasonal variation pattern both in 2007 and 2008. Two peaks of CH 4 emission were observed, the first at the tillering stage, second at panicle differentiation and heading stage. The CH 4 cumulative emission was reduced in RD by 19.3 and 19.6% in 2007 and 2008, respectively, compared with CK.