A BODIPY-based dye, OBEP, has been developed to act as a mitochondrial fluorescence probe. This dye is of high stability, low toxicity and insensitive in a pH range as wide as pH 2–10. Its uptake into mitochondria is independent of mitochondrial membrane potential in living cells. OBEP can label swollen mitochondria resulting from different degrees of cell damage in light and resist fading even after 12 h of incubation.