In this study, we found that the photoluminescence (PL) of 11-mercaptoundecanoic acid (11-MUA)-protected gold nanodots (Au NDs; ca. 2.0 nm) was highly dependent on the capping ligands and the ligand density. Deposition of 11-MUA onto the surfaces of as-prepared gold nanoparticles (Au NPs; ca. 3.0 nm) yielded luminescent 11-MUA-capped Au NDs (11-MUA-Au NDs). The PL intensity (excitation/emission: 375/525 nm) of the Au NDs decreased dramatically after purification through centrifugation (purified Au NDs are denoted herein as p11-MUA-Au NDs) as a result of a decrease in the 11-MUA ligand density on the Au NDs. Moreover, the PL intensity of the purified Au NDs was recovered after introducing new mercaptoaliphatic acid ligands (the ligand-recapped Au NDs are denoted as Au NDs@ligand; e.g., the 11-MUA recapped Au NDs are denoted as Au NDs@11-MUA). The PL intensity of the Au NDs@ligand species increased upon increasing the ligand density and chain length. Furthermore, using the Au NDs@11-MUA as a probe allowed us to detect the total concentration of mercury ions {inorganic mercury [Hg(II)] plus organic mercury (methylmercury [MeHg(I)], ethylmercury [EtHg(I)] and phenylmercury [PhHg(I)])} in aqueous solution. The selectivity of this nanosensor system for the total mercury over other metal ions is remarkably high (1000-fold), with a limit of detection (LOD, S/N = 3) for mercury ions of 2.0 nM. We have demonstrated the practicality of this approach for the determination of mercury ions in complicated biological urine and plasma samples, as well as in a fish sample (DORM II). This simple, sensitive and selective approach appears to have practical potential for use in the clinical screening of mercury ions in biofluids.