Fluorescent labeling is today of paramount importance to biological studies and numerous chemical dyes are used extensively to label biological specimens. This perspective highlights interesting aspects of fluorescent labeling by fluorescent peptides and small organic fluorophores that can be incorporated into proteins by genetic fusion to produce a fluorescent label. While many fluorescence applications rely on the use of intrinsic fluorophores, the development of new extrinsic fluorophores remains an essential element for the design of new fluorescent probes.