This article focuses on issues faced by the Indian farmers due to patenting of Genetically Modified seeds. Secondly would give a brief account of Indian legislations dealing with Seed certification and their protection and its impact on traditional farmers. Thirdly it analyzes how Indian farmers are deprived of their rights by improper governance in India. Hence, finally come to a conclusion that Globalization, Trade Related Intellectual Property Rights, Indian legislative negligence and improper implementation mechanism have had a devastating effect on Indian farmers. Neglecting protection to farmer's traditional right of seed conservation and exchange, by Indian legislators, would finally affect the sustainability of Indian agriculture, posing threat to food security and employment. This would adversely affect Indian economy. Hence, India has to make amendments in her domestic legislation and set up a mechanism at national and international level, to monitor and sort out the issues relating to farmer rights.