The proliferation of genetically modified organisms (GMOs) has become an increasingly popular subject of concern in the rapidly evolving field of agriculture. Among these, genetically modified GM(Bt) cotton stands out as a shining example of agricultural innovation, providing higher resistance and yield.Therefore, an array of critical aspects, including Consumer Driven Transparency, Regulatory Landscape and Labeling, Market Differentiation for Non-GMO Cotton, and Maintaining Supply Chain Integrity, contribute to the significance of detecting GMO cotton in today's agricultural scenario. Beyond only validating GMO presence for labeling, cotton detection tests employing RT-PCR technique serve as valuable instruments. Some innovative applications that expand their utility in the agricultural sector are Seed Purity Verification, Monitoring Potential Spread of GMO Traits, Investigating Potential Contamination Events, Geographic Mapping of GMO Cotton Distribution, and fostering Research and development for a more sustainable cotton industry.