The ongoing advancement of cultivation-independent techniques has facilitated the discovery and characterization of various microbial species and their mobile genetic elements (MGEs). Single-cell approaches, which address the limitations of metagenomics, offer invaluable insights into microbial diversity, various genetic elements, and their interactions within the microbiome. In this chapter, we introduce innovative methodologies in single-cell genomics, including a microfluidics technology and various whole-genome amplification techniques that have transformed the resolution of microbial genome sequencing. We present two high-throughput workflows for single-cell genomic analysis: the label—sort—encapsulate—amplify (LSEA) strategy and the encapsulate—amplify—label—sort (EALS) strategy. These approaches are designed for the targeted isolation and sequencing of individual single cells, enabling a comprehensive study of bacterial genomes and their MGEs, thereby enhancing our understanding of microbial ecology.