The methods and applications of a surface plasmon resonance-enhanced marking technique are disclosed. The technique uses surface plasmon resonance (SPR) excited nanoparticles and a surface plasmon resonance source in nonlinear interactions with nearby chemical substances and medium for marking purposes. The SPR-enhanced absorption and fluorescence rates of chemical substances or medium and nonlinearity of SPR interactions with chemical substances or medium make the proposed method suitable for marking fragile materials including biomaterials, such as writing on thin plastic foils or DNA-protein crosslinking. The marking method can also be applied to a three-dimensional recording and read out information system with subwavelength resolutions, coding information of secrete documents, drug delivery, tissue surgery, tattoo writing or removal, photodynamic therapy, cosmetic and dermatological treatment.