We proposed and developed a series of fluorescent methods for analysis and investigation of biological systems with a view of future biotechnological and biomedical applications. The methods we describe have been built upon several photochemical and photophysical phenomena including fluorescent quenching, photochrome photoisomerization, and energy transfer. Three new types of molecular probes have been developed and employed for such studies: (1) dual fluorophore–nitroxide compounds, (2) fluorescence–photochrome molecules, and (3) super molecules containing both fluorescence and fluorescent quenching segments. The fluorescent properties of the new probes were intensively exploited for several practical applications including a real-time analysis of antioxidants, nitric oxide, superoxide, reactive radicals, trinitrotoluene, and metal ions, investigation of molecular dynamics of biomembranes in a wide range characteristic times, detection of protein conformational transition, and characterization of surface system. Owning high sensitivity, simplicity, and availability of fluorescent techniques, these methods can be widely employed and are adaptable to fibrooptic sensoring. A general survey of the physical principles and application of the new fluorescent methods has been provided.