5-TAMRA chloride is widely used as a fluorescent dye in biological labeling and imaging applications. Its bright red-orange fluorescence makes it ideal for detecting and visualizing biomolecules such as proteins, nucleic acids, and antibodies under fluorescence microscopy. It is commonly conjugated to peptides, oligonucleotides, or other biomolecules to track cellular uptake, localization, and interactions in live or fixed cells.

Due to its high photostability and compatibility with common fluorescence detection instruments, 5-TAMRA chloride is frequently employed in assays like FRET (Förster resonance energy transfer) to study molecular interactions and conformational changes. It is also used in diagnostic probes and real-time PCR for signal reporting. The chloride salt form enhances solubility in aqueous buffers, facilitating labeling reactions in biological systems.