The article reviews the advancements and applications of metagenomics in soil microbiology, highlighting its potential to overcome the limitations of traditional techniques such as culturing and PCR-based methods. Metagenomics enables the study of microbial communities by analyzing the genetic material from environmental samples, providing insights into their diversity, function, and interactions. The review discusses the principles of metagenomics, its applications in soil microbial diversity analysis, and the effectiveness of targeted metagenomics in identifying functional genes and microorganisms. High-throughput sequencing technologies, including Sanger, Next Generation Sequencing (NGS), Illumina, and Ion Torrent, have revolutionized soil microbiome research. Third and fourth-generation sequencing systems from Oxford Nanopore Technology and Pacific Biosciences offer long-read capabilities. Complementary methods like GeoChip, clone libraries, metagenomics, and metabarcoding aid in understanding soil microbial communities. The article emphasizes the importance of metagenomics in environmental management and agriculture, despite existing limitations, and highlights its role in advancing the field of soil microbiology. Targeted metagenomics, particularly using high-throughput sequencing and stable-isotope probing, is highlighted as a powerful tool for studying specific microbial taxa and genes in complex ecosystems. The review also discusses the use of metagenomics in studying antibiotic resistance, metal resistance, and bioremediation, as well as its applications in aquatic microbial ecology and evolution. Overall, the article underscores the significance of metagenomics in advancing our understanding of soil microbiology and its ecological and environmental implications.The article reviews the advancements and applications of metagenomics in soil microbiology, highlighting its potential to overcome the limitations of traditional techniques such as culturing and PCR-based methods. Metagenomics enables the study of microbial communities by analyzing the genetic material from environmental samples, providing insights into their diversity, function, and interactions. The review discusses the principles of metagenomics, its applications in soil microbial diversity analysis, and the effectiveness of targeted metagenomics in identifying functional genes and microorganisms. High-throughput sequencing technologies, including Sanger, Next Generation Sequencing (NGS), Illumina, and Ion Torrent, have revolutionized soil microbiome research. Third and fourth-generation sequencing systems from Oxford Nanopore Technology and Pacific Biosciences offer long-read capabilities. Complementary methods like GeoChip, clone libraries, metagenomics, and metabarcoding aid in understanding soil microbial communities. The article emphasizes the importance of metagenomics in environmental management and agriculture, despite existing limitations, and highlights its role in advancing the field of soil microbiology. Targeted metagenomics, particularly using high-throughput sequencing and stable-isotope probing, is highlighted as a powerful tool for studying specific microbial taxa and genes in complex ecosystems. The review also discusses the use of metagenomics in studying antibiotic resistance, metal resistance, and bioremediation, as well as its applications in aquatic microbial ecology and evolution. Overall, the article underscores the significance of metagenomics in advancing our understanding of soil microbiology and its ecological and environmental implications.