A molecular probe that selectively tags Lck, a Src-family kinase, was developed. This probe was one of many compounds originally designed to target the active site of tyrosine kinases in general. To our surprise, however, the probe almost exclusively labeled Lck even in a lysate of Jurkat cells. This finding led us to further characterize this probe-Lck complex by a series of photolabeling and mass spectrometric analyses. The probe-binding site on Lck was located within the well-conserved region of Src-family kinases, as we originally expected. However, the unexpected selectivity of this probe toward Lck suggests that subtle factors, which are difficult to predict based on static crystal structures, play important roles in probe recognition.