A DNA probe labeled with a 4-([4-(dimethylamino)phenyl]azo)benzoic acid (DABCYL) quencher and a carboxyfluorescein (FAM) donor at its 5'- and 3'-termini can be used for the detection of Hg(2+) ions and phenylmercury ions (PhHg(+)). This DNA probe possesses a random coil structure that changes into a hairpin-like structure upon binding Hg(2+) and PhHg(+) ions. As a result, the fluorescence of the FAM unit decreased through quenching between the donor and the quencher. In the presence of ethylenediaminetetraacetic acid (EDTA), the DNA probe allowed the selective detection of PhHg(+) ions at concentrations as low as 70.0 nM, mainly as a result of T-Hg(2+)-T coordination and π-π stacking between the Ph unit and DNA bases. A linear correlation existed between the fluorescence intensity and the concentration of PhHg(+) ions over the range from 0.10 to 1.0 μM (R(2) = 0.99). After acid hydrolysis and neutralization of the samples, all of the mercury species are converted to Hg(2+) ions, allowing us to use the DNA-based probe to determine the concentrations of total mercury species at the nM level. The practicality of this probe has been validated by the analyses of pond water and fish samples, showing its advantages of sensitivity, selectivity, and simplicity.