Fluorogenic CRISPR (fCRISPR) is a novel system for imaging genomic DNA with low background fluorescence and high sensitivity. This system uses a genetically encoded fluorogenic protein that is stabilized by binding to a specific RNA hairpin. The fluorogenic protein is rapidly degraded by the proteasome unless it binds to the RNA hairpin, which is incorporated into the single guide RNA (sgRNA). This results in a ternary complex of dCas9: sgRNA: fluorogenic protein that enables fluorogenic DNA imaging. fCRISPR allows for high signal-to-noise ratio and sensitivity in imaging various genomic DNA in different human cells. It also enables tracking of chromosome dynamics and DNA double-strand breaks (DSBs) and repair in real time. fCRISPR offers a high-contrast and sensitive platform for imaging genomic loci. The system was tested in various human cell lines and showed effective labeling of genomic loci with high SNR. fCRISPR can also be used for multi-color and orthogonal imaging of genomic loci. It was shown to reveal chromosomal dynamics heterogeneity and detect telomere length. Additionally, fCRISPR enables tracking of DNA breaks and repairs in living cells. The system provides a robust and efficient platform for genomic DNA imaging with low background fluorescence and high sensitivity. The methods used for plasmid construction, cell culture, transfection, and imaging are described in detail. The results demonstrate that fCRISPR is a promising tool for genomic DNA imaging with high sensitivity and specificity.Fluorogenic CRISPR (fCRISPR) is a novel system for imaging genomic DNA with low background fluorescence and high sensitivity. This system uses a genetically encoded fluorogenic protein that is stabilized by binding to a specific RNA hairpin. The fluorogenic protein is rapidly degraded by the proteasome unless it binds to the RNA hairpin, which is incorporated into the single guide RNA (sgRNA). This results in a ternary complex of dCas9: sgRNA: fluorogenic protein that enables fluorogenic DNA imaging. fCRISPR allows for high signal-to-noise ratio and sensitivity in imaging various genomic DNA in different human cells. It also enables tracking of chromosome dynamics and DNA double-strand breaks (DSBs) and repair in real time. fCRISPR offers a high-contrast and sensitive platform for imaging genomic loci. The system was tested in various human cell lines and showed effective labeling of genomic loci with high SNR. fCRISPR can also be used for multi-color and orthogonal imaging of genomic loci. It was shown to reveal chromosomal dynamics heterogeneity and detect telomere length. Additionally, fCRISPR enables tracking of DNA breaks and repairs in living cells. The system provides a robust and efficient platform for genomic DNA imaging with low background fluorescence and high sensitivity. The methods used for plasmid construction, cell culture, transfection, and imaging are described in detail. The results demonstrate that fCRISPR is a promising tool for genomic DNA imaging with high sensitivity and specificity.