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.