Cultivation of rice, a globally important cereal crop, is a major cause of emission of the greenhouse gas (GHG) methane (CH4), giving rise to global warming. Physiological and anatomical characteristics of rice plants associated with CH4 emission were studied in six high-yielding rice varieties, Dikhow, Dishang, Jaya, Kolong, Kopilee and Lachit, during the pre-monsoon season (April–August) for 2 years (2013 and 2014) in a tropical climate in India. Significant differences (P < 0.001) in photosynthetic rate among the rice varieties were recorded and were found to influence CH4 emission from the ecosystem. Rate of CH4 emission was found correlated (r = 0.942) with size of the xylem vessels of the node of the varieties. Kolong, Lachit and Dikhow were identified as low CH4 emitters with smaller xylem vessels. The recorded GHG intensity (GHGI) revealed rice varieties as a source of GHGs, and among the varieties, Kopilee as a major source of CH4, with GHGI of 0.083 and 0.093 during 2013 and 2014, respectively. Results suggest that selection of suitable rice varieties with high grain yield accompanied by lower rate of CH4 emission can be a viable option for reduction of CH4 emissions from rice agriculture.