As a robust platform for genome editing, CRISPR/Cas9 is currently being explored for engineering biology or therapeutics, yet means for quantitative detection of Cas9 proteins remain to be fully realized. Here, we expressed Cas9 proteins and developed a novel detection method that traced Cas9 based on radiolabeled iodine. Through optimizing the reaction conditions of reaction time, temperature and cycles, we obtained 125I-Cas9 of high labeling yield. The prepared 125I-Cas9 was stable in various media and preserved excellent genome editing efficiency. Thus, our strategy provides a convenient and efficient tool for further tracing biological behaviors of Cas9 proteins in living systems.