The application of Next-Generation Sequencing (NGS) in agrigenomics has ushered in a new era of precision agriculture, enabling significant advancements in crop improvement, livestock management, and sustainable farming practices. NGS offers deep insights into the genetic makeup of plants and animals, facilitating the identification of genes associated with desirable traits such as drought resistance, yield, nutritional content, and disease resistance. This technology accelerates the breeding process by allowing for the rapid selection of individuals with optimal genetic profiles, significantly reducing the time and resources needed to develop strains and breeds that can withstand the challenges posed by climate change, pests, and diseases. Moreover, NGS aids in the understanding of plant and animal microbiomes, providing avenues to enhance growth, health, and resilience through microbiome management. In agrigenomics, NGS is not just a tool for enhancing productivity; it is a pivotal element in the pursuit of food security and sustainability, enabling the agriculture sector to meet the growing global demand for food in an environmentally friendly and sustainable manner.