Irrigated rice, represents a methane (CH4) emissions source. In rice fields, the dominance of plant-mediated transportation of CH4 from submerged soils to the atmosphere raises the possibility of varietal differences in CH4 emissions. Previous findings remain inconclusive and no study has explored varietal differences in CH4 emissions of rice in Latin America. A field experiment was conducted in Colombia to investigate the potential of a breeding line, a commercial variety, and two rice hybrids to mitigate CH4 emissions from irrigated rice. Data on CH4 emissions, phenotypic, physiological, root traits, and grain yield were collected. Results showed CH4 emissions, grain yield, root length and root surface area differences followed the order Hybrid 2 > Hybrid 1 > breeding line > Commercial variety. Whereas CH4 emissions per unit area for the two rice hybrids were within the of range 29–62% higher than the commercial variety and breeding line, CH4 emission per unit grain yield were similar across the rice genotypes. Our data suggests that differences in root development and grain yields explain genetic influence on CH4 emissions. We conclude that by exploiting differences in productivity and root characteristics among rice cultivars the transition towards low emission rice production systems can be accelerated.