Rice productivity in province of East Nusa Tenggara (ENT) is low due to the soil condition. One of the rice-producing regency in ENT is Kupang Regency with rainfed rice type. Paddy fields have also become a major source of methane emissions (CH4) as one of important greenhouse gases. This research aims to know the effect of methanotrophic bacteria application on paddy growth and methane emission at rainfed rice. Bacteria that used is Methylocystisrosea BGM 1, Methylobacter sp. SKM 14, Methylocystispalvus BGM 3 and Methylococcuscapsulatus BGM 9. This research used completely random design with threatment: (1) NPK 100% (P1), (2) NPK 50% (P2), (3) without fertilizer (P3), (4) NPK 100% + methanotrophic (P4), NPK 50% + methanotrophic (P5), and methanotrophic bacteria (P6). Gas sampling using closed chamber method.The application of methanotrophic bacteria increased the rice production. Treatment NPK 50% + methanotrophic (P5) from that rice field produced 7.0 t ha-1dry grain weight and methanotrophic bacteria treatment without NPK (P6) with improved 6.6 t ha-1dry grain weight, higher than controls of 4.9 ha-1 dry grain weight without any addition of synthetic fertilizer.The inoculation of methanotrophic bacteria increase rice production of 1.7 t ha-1.Result of methane flux measurement showed that application of methanotrophic bacteria may decrease methane emission in treatment of 100% NPK + methanotrophic (P4) (30 DAP) and treatment of 50% NPK + methanotrophic (P5) (60 DAP), -6.27 mg/m2/d and -23.87 mg/m2/d, respectively.