BODIPY-clickates, F1 and F2, for the detection of Hg(2+) have been designed, synthesized and characterized. Both F1 and F2 showed hyperchromic shifts in the UV-visible spectra in response to increasing Hg(2+) concentrations. Hg(2+) ion binding caused perturbation of the emission quenching process and chelation induced enhanced bathochromic emission of F1 and F2 to 620 nm and 660 nm, respectively. Job's plot clearly indicated that the binding ratio of F1 and F2 with Hg(2+) was 1 : 1. The NMR titration of BODIPY-clickates with Hg(2+) confirmed that aromatic amines and triazoles were involved in the binding event. Furthermore, HRMS data of F1-Hg(2+) and F2-Hg(2+) supported the formation of mercury complexes of BODIPY-clickates. The dissociation constant for the interaction between fluorescent probes F1 and F2 with Hg(2+) was found to be 24.4 ± 5.1 μM and 22.0 ± 3.9 μM, respectively. The Hg(2+) ion induced fluorescence enhancement was almost stable in a pH range of 5 to 8. Having less toxicity to live cells, both the probes were successfully used to map the Hg(2+) ions in live A549 cells.