AbstractThe molecular structure of mBDFP, a far‐red fluorescent protein (FPs) derived from an allophycocyanin homolog was resolved to 2.52 Å. Its biliverdin chromophore was found to be attached to the protein in an unusual way that was never observed in natural phycobiliproteins, and only once in a sub‐population of artificial bacteriophytochrome‐derived FPs. One of the biliverdin's vinyl groups had two cysteine residues covalently bound to its two carbon atoms. This reduces the conjugation length of the biliverdin π‐electron system, which shifts the absorption and emission spectra by about 40 nm, from the near‐infrared to the far‐red region of the spectrum. By spectrally characterizing a set of mBDFP mutants, we show that such spectral shifts can be induced by modifying a single residue in either one of two critical positions in the vicinity of the binding cysteines. This changes the reactivity of biliverdin and the cysteine's thiols towards forming one, or two thioether bonds to the vinyl group. The ability to control the spectral properties of BDFP by specific point mutations opens many possibilities for rational design of far‐red and near‐infrared FPs that are of great interest to the development of fluorescence markers for bioimaging since most biological tissues are transparent in this spectral window.