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Sialyl-Tn (STn or sialyl-Thomsen-nouveau) is a carbohydrate antigen expressed by more than 80% of human carcinomas. We here report a strategy for ratiometric STn detection and dual-color cancer cell labeling, particularly, by molecularly imprinted polymers (MIPs). Imprinting was based on spectroscopic studies of a urea-containing green-fluorescent monomer 1 and STn-Thr-Na (sodium salt of Neu5Acα2-6GalNAcα-O-Thr). A few-nanometer-thin green-fluorescent polymer shell, in which STn-Thr-Na was imprinted with 1, other comonomers, and a cross-linker, was synthesized from the surface of red-emissive carbon nanodot (R-CND)-doped silica nanoparticles, resulting in dual fluorescent STn-MIPs. Dual-color labeling of cancer cells was achieved since both red and green emissions were detected in two separate channels of the microscope and an improved accuracy was obtained in comparison with single-signal MIPs. The flow cytometric cell analysis showed that the binding of STn-MIPs was significantly higher (p < 0.001) than that of non-imprinted polymer (NIP) control particles within the same cell line, allowing to distinguish populations. Based on the modularity of the luminescent core-fluorescent MIP shell architecture, the concept can be transferred in a straightforward manner to other target analytes.