Hybrid seeds are essential in modern agriculture, for enhancing crop yields, disease resistance, and overall quality. Produced through controlled crossbreeding of genetically distinct parents, these seeds inherit desirable traits, improving resilience against environmental stress and leading to uniform crop yield. Maintaining the genetic purity of hybrid seeds is crucial for ensuring their integrity and reliability. Genetic purity testing is a key aspect of hybrid seed production, identifying and quantifying impurities that may arise. Techniques such as morphological analysis, biochemical markers, and DNA-based methods are employed to ensure accurate testing. While morphological and biochemical methods provide insights, they can be influenced by environmental factors and have limitations in definitively proving hybridity. Molecular methods, which analyze DNA sequences, offer a more precise approach to testing, enabling early detection of seed hybridity and exhibiting reproducibility. Molecular markers like RFLP, AFLP, RAPD, SSR, and SNP have greatly improved plant breeding and genetic purity testing, providing high precision in identifying genetic impurities in hybrid seed lots particularly, off-types like pollen shedders. Despite the progress in molecular techniques, challenges such as complexity, costs, and the need for standardization persist. Addressing these issues are critical to ensuring that molecular markers continue to play a vital role in maintaining the quality and sustainability of global seed supply chains.