Techniques for labeling proteins with small molecules have attracted the attention of many life scientists. We have developed a novel protein labeling system that combines a genetically modified, noncatalytic β-lactamase variant and specific mechanism-based fluorescent probes. Rational design of the tag protein and the labeling probes enables highly specific incorporation of the fluorogen. The feasibility of our approach was confirmed by gel electrophoresis, mass spectrometry, fluorescence spectroscopy, and fluorescence microscopic imaging. Labeling techniques that satisfy the dual criteria of specificity and fluorogenicity have rarely been reported. As a consequence, this method could be a broadly useful research tool in the field of life science.