CDy9 is a highly selective fluorescent probe for the detection and isolation of mESC using fluorescence microscopy and flow cytometry. CDy9 allows the detection and isolation of intact stem cells with marginal impact on their function and capabilities. CDy9 may be a non-invasive biotechnological tool for the preparation, purification and characterization of mESC. Stem cell research has gathered immense attention in the past decade due to the remarkable ability of stem cells for self-renewal and tissue-specific differentiation. Despite having numerous advancements in stem cell isolation and manipulation techniques, there is a need for highly reliable probes for the specific detection of live stem cells.