Abstract A BODIPY-based (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene, TMB) green fluorescent probe for quantitative real-time polymerase chain reaction (qPCR) was synthesized by azide-alkyne cycloaddition. Comparative studies with the analogous fluorescein-based probe were carried out. We demonstrated that fluorescent probes with the TMB fluorophore can be used in qPCR experiments.