CRISPR-Cas9 technology has revolutionized biological research, particularly in medical research, biotechnology, and agriculture. Initially known as a bacterial immune system against viral infections, the programmable Cas9 enzyme has expanded its applications beyond gene editing to include gene regulation, epigenetic editing, chromatin engineering, and imaging. This review provides a brief history of gene-editing tools and describes the wide range of CRISPR-based genome-targeting tools. It highlights the development of targeted nucleases, such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), which were followed by the discovery and utilization of CRISPR-Cas9. The review discusses the evolution of CRISPR systems, including the classification of CRISPR types and the discovery of Cas9 variants with different PAM requirements and substrate preferences. It also covers the re-engineering of CRISPR-Cas9 tools to improve targeting specificity and reduce off-target effects. The review further explores the applications of CRISPR-Cas9 beyond genome editing, such as base editing, gene expression regulation, epigenome editing, and live cell chromatin imaging. Finally, it discusses the inherent limitations and future directions of CRISPR technologies, emphasizing their broad impact on science, medicine, and biotechnology.CRISPR-Cas9 technology has revolutionized biological research, particularly in medical research, biotechnology, and agriculture. Initially known as a bacterial immune system against viral infections, the programmable Cas9 enzyme has expanded its applications beyond gene editing to include gene regulation, epigenetic editing, chromatin engineering, and imaging. This review provides a brief history of gene-editing tools and describes the wide range of CRISPR-based genome-targeting tools. It highlights the development of targeted nucleases, such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), which were followed by the discovery and utilization of CRISPR-Cas9. The review discusses the evolution of CRISPR systems, including the classification of CRISPR types and the discovery of Cas9 variants with different PAM requirements and substrate preferences. It also covers the re-engineering of CRISPR-Cas9 tools to improve targeting specificity and reduce off-target effects. The review further explores the applications of CRISPR-Cas9 beyond genome editing, such as base editing, gene expression regulation, epigenome editing, and live cell chromatin imaging. Finally, it discusses the inherent limitations and future directions of CRISPR technologies, emphasizing their broad impact on science, medicine, and biotechnology.