Several fluorescent protein exist in nature, but the most important one as a research tool is Green Fluorescent Protein (GFP) from the jellyfish Aequorea victoria, which spontaneously fluoresces upon folding via specific serine-tyrosine-glycine residues. The benefit that GFP and other fluorescent proteins have over organic dyes or quantum dots is that they can be expressed exogenously in cells alone or as a fusion protein, a protein that is created by ligating the fluorescent gene (e.g., GFP) to another gene and whose expression is driven by a housekeeping gene promoter or another specific promoter. This approach allows fluorescent proteins to be used as reporters for any number of biological events, such as sub-cellular localization and expression patterns.
A variant of GFP is naturally found in corals, specifically the Anthozoa, and several mutants have been created to span the visible spectra and fluoresce longer and more stably.
Other proteins are fluorescent but require a fluorophore cofactor, and hence can only be used in vitro; these are often found in plants and algae (phytofluors, phycobiliprotein such as allophycocyanin).