Historically, the onset of green revolution that led to the introduction of high-yielding varieties (HYV) seeds rewrote the growth story of Indian agriculture. In the long term side effects of intensive farming were realized. In the meanwhile this success led to introduction of Bacillus Thuringiensis (Bt) cotton in India. Since then various divergent voices are being raised to protect traditional seed holding rights of the farmers. The policy paralysis due to elusive fear of patent rights has contributed to stalemate in embracing Genetically Modified (GM) crops. The study finds that the heightened scrutiny due to those fears brought new evidence about non-viability of such crops for Indian conditions. The agriculture sector has overcome the stalemate and is silently evolving to embrace its vast cultural knowledge and biodiversity along with non GM technology. The study is centered on the role of trade related aspects of intellectual property rights (TRIPS) and its impact on agricultural innovation lead by traditional knowledge and biotechnology. The data extracted from RBI, FAO and UNCOMTRADE WITS suggests that the share of primary products in the total exports is on decline. Similarly, the yield of Bt Cotton has become stagnant after an initial increase till 2004. After critically analyzing the reasons for current decline, the study suggests a relook at innovation by increasing the research and development (R&D) expenditure in traditional knowledge (TK) and biotechnology by both public and private stakeholders.