Autophagy is an important cellular process of self-degradation for dysfunctional or unnecessary molecules and organelles, thus dysregulation of autophagy can be involved in various diseases such as neurodegenerative diseases. To understand complex process of autophagy and the related diseases, various methods have been developed, for example biochemical, chemical, and imaging assays. In particular, fluorescent protein (FP)-based autophagy biosensors allow sensitive and selective monitoring of autophagy progression in live cells. After the discovery of green fluorescent protein (GFP), a variety of FPs has been discovered and engineered which have different physicochemical properties, such as excitation/emission spectra, Stokes shift, maturation rate, stability, photo-reactivity and pH-sensitivity. Advances in fluorescent protein technology and FP-based biosensors enabled the real-time monitoring of cellular and molecular events in live cells with high spatiotemporal resolutions.