We have chemically modified cellulose nanofibrils (CNF) with furan and maleimide groups, and selectively labeled the modified CNF with fluorescent probes; 7-mercapto-4-methylcoumarin and fluorescein diacetate 5-maleimide, through two specific click chemistry reactions: Diels-Alder cycloaddition and the thiol-Michael reaction. Characterization by solid-state (13)C NMR and infrared spectroscopy was used to follow the surface modification and estimate the substitution degrees. We demonstrate that the two luminescent dyes could be selectively labeled onto CNF, yielding a multicolor CNF that was characterized by UV/visible and fluorescence spectroscopies. It was demonstrated that the multicolor CNF could be imaged using a confocal laser scanning microscope.