Strontium-90 is one of the most frequently released radioactive products in waste discharged from nuclear reactors. With a long half-life and chemical similarity to calcium, this radioisotope takes hundreds of years to decay to negligible levels and can accumulate in the food chain and bones, resulting in serious health hazards. As a result, there is growing interest in its fate and dispersion in the environment. However, the identification of 90Sr remains a challenge due to the absence of characteristic energy rays signifying its presence. Here we show a biosensor that enables the detection of Sr2+ ions in an ultrasensitive and highly selective manner. Our approach takes advantage of a fluorogenic dye, thioflavin T, which triggers the folding of DNA to form guanine-quadruplex structures. Owing to the high binding affinity of this DNA structure, on exposure to a trace amount of Sr2+ ions, thioflavin T is readily replaced, leading to attenuation of the fluorescence intensity and a detection limit of 2.11 nM. Our work could contribute to the sustainability of nuclear power by providing a technological solution to monitor the transportation of radioactive strontium pollution in the environment, a notable advance, especially after the recent Fukushima nuclear incident.