We have created series of novel, water-soluble, alkanethiol-AuNPs whose fluorescence wavelength is tunable through modification of the chain length of the alkanethiols. The highly fluorescent alkanethiol-AuNPs, such as the 11-MUA-AuNPs, are easily purified and are capable of sensing mercury(II) ions based on fluorescence quenching through mercury(II)-indued aggregation of AuNPs. The sensitivity of the 11-MUA-AuNPs toward mercury(II) was high (LOD = 5.0 nM), with remarkable selectivity over other metal ions in aqueous solution.