This manuscript describes a highly selective and ultra sensitive determination of Hg(II) in aqueous solution using functionalized mercaptothiadiazole capped silver nanoparticles (AgNPs) by spectrofluorimetry. We have synthesized 2,5-dimercapto-1,3,4-thiadiazole (DMT), 2-mercapto-5-methyl-1,3,4-thiadiazole (MMT) and 2-mercapto-5-amino-1,3,4-thiadiazole (AMT) capped AgNPs by wet chemical method. Among these AgNPs, DMT capped AgNPs (DMT-AgNPs) were more stable and highly fluorescent than the other two AgNPs. DMT-AgNPs show the emission maximum at 677nm while exciting at 400nm. After the addition of Hg(II), the emission intensity was decreased at 677nm. The observed decreased emission intensity was ascribed to the aggregation of AgNPs and it was confirmed by TEM. Based on the decrease in emission intensity, the concentration of Hg(II) was determined. The lowest detection limit (LOD=3S/m) of 1.0pgL⁻¹ was achieved for the first time using DMT-AgNPs by spectrofluorimetry. The quantum yield (ϕ_F), Stern–Volmer constant (K_SV), Gibbs free energy changes (ΔG°), association constant (K_f) were calculated and the quenching mechanism also was discussed. Finally, the proposed method was successfully utilized for the determination of Hg(II) in river water, industrial effluent water and tap water samples. The obtained results were fairly matches with the ICP-AES method.