Inspired by the high affinity between heavy metal ions and bio-molecules as well as the low toxicity of carbon-based quantum dots, we demonstrated the first application of a DNA derived carbonaceous quantum dots, namely bio-dots, in metal ion sensing. The present DNA-derived bio-dots contain graphitic carbon layers with 0.242 nm lattice fringes, exhibit excellent fluorescence property and can be obtained via a facile hydrothermal preparation procedure. Hg(II) and Ag(I) are prone to be captured by the bio-dots due to the existence of residual thymine (T) and cytosine (C) groups, resulting in a quenched fluorescence while other heavy metal ions would cause negligible changes on the fluorescent signals of the bio-dots. The bio-dots could be used as highly selective toxic-free biosensors, with two detecting linear ranges of 0-0.5 mu M and 0.5-6 mu M for Hg(II) and one linear range of 0-10 mu M for Ag(I). The detection limits (at a signal-to-noise ratio of 3) were estimated to be 48 nM for Hg(II) and 0.31 mu M for Ag(I), respectively. The detection of Hg(II) and Ag(I) could also be realized in the real water sample analyses, with satisfying recoveries ranging from 87% to 100%. (C) 2015 Elsevier B.V. All rights reserved.