Apoptosis plays crucial roles during development and in disease conditions. While there are some methods to detect apoptosis in vitro, most of them are end-point assays which cannot be used to detect apoptosis in the physiological context of live animals. In this study, transgenic sensor zebrafish were generated that specifically produce a fluorescence resonance energy transfer (FRET)-based biosensor in zebrafish skin. Under normal condition, the skin cells of the sensor zebrafish emit green fluorescence; when caspase-3 is activated during apoptosis, the skin cells of the sensor zebrafish switch to emit blue fluorescence. Through time-lapse FRET imaging with the sensor zebrafish, we observed that caspase-3 can be activated within 5 minutes (min) and apoptosis can be completed in around 30 min in live zebrafish, no matter the apoptosis occurs several hours post UV irradiation or during the normal development. Using the sensor zebrafish, we found that apoptosis can occur in different parts of the zebrafish skin including the skin covering trunk, eye, yolk sac and head during development. Interestingly, we observed that the yolk sac diameter of zebrafish reduced from 723.8±25.1 µm at 24 hours post-fertilization (hpf) to 346.1±24.6 µm at 120 hpf. To accommodate this dramatic reduction of the yolk sac size, we found that some excess skin cells on the surface of yolk sac were removed by apoptosis during this process. The sensor zebrafish provide a powerful and convenient tool for non-invasive and real-time detection of apoptosis at single-cell resolution in live zebrafish.