This chapter explores the use of transcriptomic analysis to identify genes in microorganisms that suppress pathogens. By studying gene expression patterns, researchers can understand the molecular mechanisms underlying biocontrol. Various functional categories of biocontrol genes are discussed, including antibiotic production, hydrolytic enzyme production, competition, plant growth promotion, and immune system function. Transcriptional profiling techniques, such as RNA sequencing (RNA-Seq), provide a comprehensive view of gene expression changes. This chapter highlights the importance of understanding the temporal and spatial dynamics of gene expression and the value of comparative transcriptomics in identifying genes associated with effective biocontrol. Functional annotation of differentially expressed genes using Gene Ontology (GO) terms, protein family mapping, and pathway enrichment analysis helps elucidate their potential roles in biocontrol. This chapter also discusses the integration of transcriptomics with other omics approaches and systems biology methods. Finally, the importance of experimental validation to confirm the functions of candidate biocontrol genes and assess their efficacy in suppressing pathogens is emphasized.