Endosymbionts are types of microorganisms that reside within the cells of a host and play a vital role in host biology, including nutrition, defense, and development. Some endosymbionts can be found either inside cells or attached to the surface of cells. Metagenomics is a recently used technique for the analysis of environmental microorganisms. Metagenomics analysis and next-generation sequencing played important roles in the identification and characterization of endosymbionts. This chapter elaborates on endosymbiont isolation, purification, and amplification of genome sequencing. Metagenomics sequencing analysis was performed for the identification of endosymbiont.