Boron difluoride (BF2) complex dyes are relatively non-polar and electrically neutral tending to reduce the perturbation of the conjugate functional characteristics. Consequently, they are frequently the favored choice for biological labeling. Also, their conjugates of low molecular weight structures are more likely to be permeable to live cells than other conjugates of charged chromophores. As a result of their high extinction coefficient, another significant application of boron difluoride complexes is their reactivity and high detection ability to volatile amine reagents accessible for HPLC and electrophoresis. They are more useful than the majority of other dyes with long absorption wavelength. BF2 complex conjugates are extremely valuable reagents for many bio-analytical screening purposes, such as their affinity to quench the fluorescence upon conjugation to certain biopolymers. In this review, we discuss the preparation of boron difluoride carbonyl based-complexes, including O-O double-dentate and N-O double-dentate dyes, as well as shedding light on their photophysical properties.