Integration of metagenomics with genome editing represents a promising direction for addressing challenges in agriculture, biotechnology, and environmental protection. Genome editing exhibits significant role in agriculture, focusing on crop improvement for stress tolerance, disease resistance, and nutritional enhancement. Metagenomics allows for the exploration of genetic material from a diverse array of non-cultivable microorganisms, leading to the discovery of novel genes, pathways, and genomes. Metagenomics significantly enhances our understanding of genetic diversity, which is crucial for genome editing purposes. The integration of metagenomics with genome editing shows promising applications in developing improved crops, engineering microorganisms for environmental protection, and advancing biotechnology. The continued development of computational tools and analytical methods for metagenomic data analysis, combined with advances in genome editing techniques, suggests a future where genetic modifications can be made with greater precision, efficiency, and confidence in their outcomes. This chapter explores the intersection of metagenomics and genome editing technologies, highlighting their synergistic relationship in advancing genetic research and applications.