In 2012, it was discovered that precise gene editing could be induced in the target DNA using the reprogrammable characteristics of the CRISPR system. Since then, several studies have investigated the potential of the CRISPR system to edit various biological organisms. For the typical CRISPR system obtained from bacteria and archaea, many application studies have been conducted and have spread to various fields. To date, orthologs with various characteristics other than CRISPR-Cas9 have been discovered and are being intensively studied in the field of gene editing. CRISPR-Cas12 and its varied orthologs are representative examples of genome editing tools and have superior properties in terms of in vivo target gene editing compared to Cas9. Recently, TnpB and Fanzor of the OMEGA (obligate mobile-element guided activity) system are identified to be the ancestor of CRISPR-Cas12 based on phylogenetic analysis. Notably, the compact sizes of Cas12 and OMEGA endonucleases allows adenosine-associated virus (AAV) delivery, hence, they are set to challenge Cas9 for in vivo gene therapy. This review will focus on these RNA-guided reprogrammable endonucleases: their structure, biochemistry, off-target effects, and applications in therapeutic gene editing.