Mercury is a highly toxic heavy metal, and detection of Hg(2+) by biosensors has attracted extensive research interest in the past decade. In particular, a number of DNA-based sensing strategies have been developed. Well-known examples include thymine-Hg(2+) interactions and Hg(2+)-activated DNAzymes. However, these mechanisms are highly dependent on buffer conditions or require hybridization with another DNA strand. Herein, we report a new mechanism based on Hg(2+)-induced cleavage of phosphorothioate (PS) modified RNA. Among the various metal ions tested, Hg(2+) induced the most significant cleavage (∼16%), while other metals cleaved less than 2% of the same substrate. The uncleaved substrate undergoes desulfurization in the presence of Hg(2+). This cleavage reaction yields a similar amount of product from pH 3.5 to 7 and in the temperature range between 20 and 90 °C. Various PS RNA junctions can be cleaved with a similar efficiency, but PS DNA junctions cannot be cleaved. A molecular beacon containing three PS RNA modifications is designed, detecting Hg(2+) down to 1.7 nM with excellent selectivity. This sensor can also detect Hg(2+) in the Lake Ontario water sample, although its response is significantly masked by fish tissues.