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Mercury ion (Hg2+) is recognized as one of the most toxic metal ions for the environment and for human health. Techniques utilized in the detection of Hg2+ are an important factor. Herein, a simple thymine was successfully employed as the surface enhanced Raman spectroscopy sensor for Hg2+ ion detection. The limit of detection (LOD) of the developed sensor is better than 0.1 nM (0.02 ppb). This sensor can also selectively distinguish Hg2+ ions over 7 types of alkali, heavy metal and transition-metal ions. Moreover, the LOD of the sensor can even achieve 1 ppb in practical application in the nature system, which is half the maximum allowable level (10 nM, 2 ppb) stipulated in the US Environmental Protection Agency standard. Further investigation of the thymine-Hg2+-thymine coordination mechanism provides a possible means of detecting other metal ions by replacing the metal ion-specific ligands. This work paves the way for the detection of toxic metal ions and environmental problems.