This study describes the design, synthesis and spectral behaviour of a fluorescent molecular sensor which is able to recognize Hg2+ and Au3+ ions via different emission modes. Determination of identity and amount of heavy metal ions has crucial importance for scientific researches. Detection of trace metal ions can be achieved by classical spectroscopic methods such as atomic absorption and atomic emission spectroscopy and inductively-coupled plasma spectrometry. In contrast to these highly expensive and time consuming methods, fluorogenic or chromogenic methods provide an alternative way for the detection of these species. There are many organic molecules that act as signaling unit for fluorogenic sensing strategy such as rhodamine, fluorescein, coumarin and BODIPY derivatives. Among these, BODIPY fluorophore was chosen for this work as a signal reporter due to its unique properties. In this research, the detection of Hg(II) and Au(III) ions was recognized in two distinct fluorescence changes: one resulting from a reversible Hg2+/sensor complex formation, the other an irreversible Au3+-mediated hydrolysis reaction. The minimum amount of Au(III) and Hg(II) ions detectable in aqueous solution was determined to be 128 nM and 160 nM, respectively. The capacity of the developed probe for imaging was studied in living cells. The investigation showed that the probe can be used efficiently for in vitro imaging of Au3+ and Hg2+ species.