A damaged ecosystem must be rebuilt to its original form, or a new ecosystem must be created in a degraded area. Ecosystem restoration is a complex procedure. Researchers can now investigate the structure and function of ecosystems at the molecular level thanks to the development of molecular techniques as a potent tool for ecosystem restoration. This chapter examines the application of molecular methods to ecosystem regeneration. The various available molecular methods and how they have been applied to monitor ecosystem health, identify microbial communities in ecosystems, and comprehend interactions between microbes and plants are discussed. The chapter also examines the application of molecular methods to the restoration of ecosystems that have been damaged, including the use of plant-microbe interactions to promote plant development in contaminated soils. The chapter emphasizes the significance of molecular methods in ecosystem restoration and their potential to offer a more precise and thorough comprehension of ecosystem processes. The conclusion highlights the importance of ongoing investigation into the use of molecular methods for ecosystem restoration, especially in creating novel methods and their incorporation with existing restoration techniques. In the end, applying molecular methods can help develop practices for ecological restoration that are more efficient and long-lasting.