DNA-templated silver nanoclusters (DNA-Ag NCs) with cytosine (C)-rich sequences (four or more segments of consecutive (2–5) C-bases) were synthesized. They display green and/or orange/red emissions under different excitation wavelengths. There is indication that more consecutive C-bases lead to longer emission wavelengths. The ratio of the red and green emissions of the DNA-Ag NCs depends on whether the NCs were synthesized under acidic or basic conditions. We also prepared the DNA copper/silver nanoclusters (DNA-Cu/Ag NCs) which can be synthesized in shorter time and display higher stability. The DNA-Cu/Ag NCs, under 470 nm photoexcitation, always display green emission, with a peak at 550 nm, irrespective of whether being prepared under acidic or basic conditions. The fluorescence of the Cu/Ag NCs is selectively quenched by Hg(II) ions which can be quantified by this nanoprobe with a detection limit as low as 2.4 nM. The quenching mechanism was studied by Stern-Volmer plots and lifetime studies which revealed that both static and dynamic quenching are operative.