The Green House Gas Emission (GHGs) from the carp culture ponds (n = 12) of West Godavari, Krishna, and Guntur districts of Andhra Pradesh and from the ponds (n = 4) of Moyna, East Medinipur district of West Bengal, India was assessed through carbon storage and carbon footprint analysis. The average inputs as Carbon Equivalent (CE) were 14407 ± 2651, and 9231 ± 1007 kg/ha in Andhra Pradesh, and West Bengal, respectively. The average carbon storage were 6216 ± 2291, and 5360 ± 1439 kg/ha, in Andhra Pradesh, and Moyna, West Bengal respectively. The emissions of CO2-e and CH4-e were 1.91 ± 0.42 kg CO2-e/kg fish and 0.122 ± 0.027 kg CH4-e/kg fish, respectively in Andhra Pradesh. The emissions of CO2-e and CH4-e were 0.006 to 2.07 (average 0.72) kg CO2-e /kg fish, and 0.0004 to 0.132 (average 0.046) kg CH4-e /kg fish production, respectively in Moyna, West Bengal.