A colorimetric assay has been developed for the simultaneous selective detection of silver(I) and mercury(II) ions utilizing metal nanoparticles (NPs) as sensing element based on their unique surface plasmon resonance properties. In this method, sulfhydryl group modified cytosine-(C)-rich ssDNA (SH-C-ssDNA) was self-assembled on gold nanoparticles (AuNPs) to produce the AuNPs-C-ssDNA complex, and sulfhydryl group modified thymine-(T)-rich ssDNA (SH-T-ssDNA) was self-assembled on silver nanoparticles (AgNPs) to produce the AgNPs-T-ssDNA complex. Oligonucleotides (SH-C-ssDNA or SH-T-ssDNA) could enhance the AuNPs or AgNPs against salt-induced aggregation. However, the presence of silver(I) ions (Ag(+)) in the complex of ssDNA-AuNPs would reduce the stability of AuNPs due to the formation of Ag(+) mediated C-Ag(+)-C base pairs accompanied with the AuNPs color change from red to purple or even to dark blue. Moreover, the presence of mercury(II) ions (Hg(2+)) would also reduce the stability of AgNPs due to the formation of Hg(2+) mediated T-Hg(2+)-T base pairs accompanied with the AgNPs color change from yellow to brown, then to dark purple. The presence of both Ag(+) and Hg(2+) will reduce the stability of both AuNPs and AgNPs and cause the visible color change. As a result, Ag(+) and Hg(2+) could be detected qualitatively and quantitatively by the naked eye or by UV-vis spectral measurement. The lowest detectable concentration of a 5 nM mixture of Ag(+) and Hg(2+) in the river water was gotten by the UV-vis spectral measurement.