A novel BODIPY-based near-IR emitting probe as a selective and sensitive fluorophore for Hg(II) is synthesized. This versatile BODIPY fluorophore is functionalized for long wavelength emission at the 3 and 5 positions via a condensation reaction in which two dithiodioxomonoaza-based crown-containing phenyl units are conjugated to the BODIPY core as a chelating unit. This designed fluorophore, employing an ICT sensor can be used effectively to detect Hg(II) cations by way of a hypsochromic shift (∼90 nm) in both the absorption and emission spectra. © 2009 Elsevier Ltd. All rights reserved.