The utilization of subtractive genomic analysis has emerged as an important and essential method in modern drug discovery and development since it significantly improves the process of identifying and validating potential targets for discovering novel therapeutic compounds to treat severe infections caused by Antimicrobial-resistant (AMR) - pathogenic species. This review provides a complete overview of the methodology, advantages, disadvantages, and prospects, associated with subtractive genomic research in the context of drug discovery and development. The initial phase of analysis encompasses the retrieval of data, which serves as a foundation for the subsequent data mining process in Phase 1. After data mining, Phase 2 utilizes subtractive channels for the target's non-homology and essentiality analysis. Phase 3 of the study aims to provide a comprehensive understanding of prospective targets by their qualitative characterization. Further, Phase 4 of the study emphasizes on conducting structure-based analyses, which involves the determination, refinement, evaluation, and validation of three-dimensional structures of the target proteins, along with their active site prediction and selection of the novel therapeutic compounds against that active site on the obtained targets through virtual screening and docking studies by utilizing various databases and servers. The therapeutic compounds obtained can be then validated by and testing, thereby establishing a connection between the computational predictions and real applications.