Cancer stem cells (CSCs) have been identified in several tumor tissues. Since CSCs are resistant to cancer therapies, including chemotherapy and radiation therapy, and can even remain after therapies, tumor tissue often regrows and relapses. Thus, identification of CSCs and treatment targeting CSCs are required to treat tumor tissues. Reportedly, a fluorescent vector consisting of fluorescein ZsGreen fused to the carboxyl-terminal region of ornithine decarboxylase (cODC) was used to detect CSCs or therapy-resistant cancer cells in tumor tissues of the brain, pancreas and liver. Cells transfected with the fluorescent vector can express a fluorescein fused to cODC and become fluorescent only when the fusion protein is accumulated. In the present study, CSCs or therapy-resistant cancer cells were identified with the fluorescent vector in esophageal squamous cell carcinoma. The use of this fluorescent vector in drug screening enabled the detection of three drugs, AKT inhibitor XI, ERK inhibitor II and JAK inhibitor I, which target malignant CSCs.