Recently, fluorescent probes have been intensively developed to detect specific biomolecules and monitor biological events. In particular, many probes based on bis(Zn2+-dipicolylamine) complex have been synthesized to detect phosphate-containing biomolecules because this complex strongly binds to phosphate or diphosphate groups in water. There are many different kinds of phosphate-containing biomolecules that may play critical roles in a living system. Therefore, there is a real need to develop selective probes, not only for the detection of biological phosphates, but also for cell imaging, enzyme assay, and disease diagnosis. Herein we report our recent efforts towards the development of selective fluorescent probes especially for biological phosphates (PPi, ppGpp, phosphatidylserine, siRNA, etc.). We also demonstrate a highly selective sensing system for flavins based on the photo-oxidation of a xanthene ring in the probe. This is the first example of optical flavin detection by fluorescence signals emitted from the oxidized form of a synthetic probe, and not from the intrinsic green fluorescence of an isoalloxazine moiety of flavins. This novel approach enabled us to monitor flavins more clearly for a relatively long period. The applicability of the probe to flavin-linked biological events was demonstrated through quantification of FAD in human serum, in vitro cellular imaging of eosinophils and mitochondrial flavins, as well as monitoring mitochondrial flavin’s redox balance in tissue. Furthermore, a cell lysate test suggested that eosinophilia samples could be distinguished from normal samples by the display of different fluorescence intensities. This sensing system, based on the redox mechanism, is expected to be an alternative method used to overcome drawbacks found while detecting redox-active biological targets in previous investigations.