It is an object of the present invention to obtain a labeled protein, and specifically, to separate a labeled protein and the same unlabeled protein. There is provided a labeled protein including: a protein to be labeled having a target protein, at least one or more affinity interaction domains for binding to an affinity support, and at least one or more labeling sites; and a labeling reagent binding to at least one of the labeling sites; wherein the affinity of the labeled protein for the affinity support is difference from that of the protein to be labeled for the affinity support.