The in vivo incorporation of non-natural amino acids into specific sites within proteins has become an extremely powerful tool for bio- and protein chemists in recent years. One avenue that has yet to be explored, however, is whether or not the incorporation of non-natural amino acids can tune the color of light emitted by bioluminescent proteins, whose light emission mechanisms are more complex and less well understood than their fluorescent counterparts. Bioluminescent proteins are becoming increasingly important in a variety of research fields, such as in situ imaging and the study of protein-protein interactions in vivo, and an increased spectral variety of bioluminescent reporters is needed for further progress. Thus, herein we report the first successful spectral shifting (44 nm) of a bioluminescent protein, aequorin, via the site-specific incorporation of several non-natural amino acids into an integral amino acid position within the aequorin structure in vivo.