A multisignaling Hg(II) sensor based on a benzimidazole substituted BODIPY framework was designed, which displays excellent selectively toward Hg(II) in vitro and in vivo. Optical and fluorogenic measurements in solution reveal that the sensor can detect mercury ions at submicromolar concentrations, with high specificity. The detection of Hg(II) is associated with a blue-shift in optical spectra and a simultaneous increase in the fluorescence quantum yield of the sensor, which is attributed to a decrease in charge delocalization and inhibition of photoinduced electron transfer upon binding to Hg(II). Using several spectroscopic measurements, it is shown that the binding mechanism involves two sensor molecules, where lone pairs of the benzimidazole nitrogen coordinate to a single mercury ion. The utility of this BODIPY sensor to detect Hg(II) in vivo was demonstrated by fluorescence imaging and spectroscopy of labeled human breast adenocarcinoma cells. While average emission intensity of the sensor over a large number of cells increases with incubated mercury concentrations, spatially resolved fluorescence spectroscopy performed on individual cells reveals clear spectral blue-shifts from a subensemble of sensors, corroborating the detection of Hg(II). Interestingly, the emission spectra at various submicrometer locations within cells exhibited considerable inhomogeneity in the extent of blue-shift, which demonstrates the potential of this sensor to monitor the local (effective) concentration of mercury ions within various subcellular environments.