The current scenario of global climate change has severely influenced the edaphic factors that have negatively affected the agriculture system. However, a beautiful symbiotic relationship between plant and microbes alleviates the plant response to the adverse effects of harsh environmental conditions. This relationship is generally governed by a complex molecular cross-talk between plants and the microbial community, wherein the plants provide shelter and food to micro-organisms and, in return, the microbes assist plants in water and nutrients absorption during environmental adversities. To unravel this complex plant-microbial cross-talk, the next-generation sequencing (NGS) approach has emerged as a boon. The NGS has assisted in identification of novel genes and their expression profiles to dissect a variety of trait in all the domains of life. In this chapter we focus on the NGS platform for meta-transcriptomics and metagenomics data to understand complex plant-microbes communication during the symbiotic association. The chapter also provides a quick overview of sample library preparation, sequencing, and pipelines used for metagenomics/meta-transcriptomics data analysis and acts as a guide for investigating the molecular basis of plant-microbe interaction.