Abstract: A field experiment was conducted to explore the effects of genetically modified rice with Hvsusiba2 gene on paddy field methane mitigation. Hvsusiba2 gene is a transcription factor that acts on the upstream of starch synthesis pathway and is recognized as a key regulator for barley starch accumulation and assimilation distribution. Previous studies have shown that japonica rice (Oryza sativa L. subsp. japonica) integrated with Hvsusiba2 gene significantly reduces methane emission in paddy fields and increases content of seed starch. To further understand gene effects on cutting down of methane emissions under different rice genetic conditions, we introduced Hvsusiba2 into indica rice (O. sativa L. subsp. indica) and then investigated methane emissions from Hvsusiba2 rice field as well as the population size of bacteria associated with methane emissions in paddy fields during the growing season from April to September 2016. The results showed that the range of methane mitigation for the whole season was 54.7%-3.8%, compared with the control (wild rice). The highest mitigation rate was during booting period, reaching 54.7%. Total methane emissions of the two lines of Hvsusiba2 rice were respectively 5 060.16 mg·m^-2 and 5 250.60 mg·m^-2, while that under wild rice was 7 249.68 mg·m^-2 for the period from the first measurement to harvest. Methane reduction rates of the two lines were 30.30% and 27.58%, respectively. The abundance of 6 orders or families of methanogens and 2 groups of methanotrophs in Hvsusiba2 rice fields showed significant (P < 0.05, P < 0.01) decreases almost throughout the entire growing season when Hvsusiba2 rice was compared with wild rice. In addition, total bacteria populations during rice tillering, heading and flowering periods were significantly (P < 0.05, P < 0.01) lower in Hvsusiba2 rice than in wild rice. Population size of 6 methanogens were in the order of:Methanosaetaceae (Mst) > Archaea (ARC) > methanogens (MET) > Methanomicrobiales (MMb) > Methanosarcinaceae (Msc) > Methanobacteriales (MBT). Among these, Methanosaetaceae had the largest community, followed by Archaea. Of the 2 groups of methanotrophs, the abundance of MBAC was much larger than that of TYPE Ⅱ. After comparison of our experimental data with other studies, we concluded that Hvsusiba2 rice mechanism for reducing methane emission more likely regulated carbohydrate flow to ground parts of the plant, reduced assimilates transported to soil and lowered methane-related bacteria abundance, which ultimately reduced methane emissions.