A biphenyl derivative containing two D-Ala-D-Ala moieties was found to form fluorescent nano/microfibers when subjected to self-assembly conditions in aqueous EtOH. Incubation of the nano/microfibers with vancomycin results in the disappearance of the fibers along with a significant decrease in the fluorescence intensity. The detection limit of vancomycin determined by the fluorescence quenching strategy was calculated to be ca. 57 μM. Regeneration of the original fiber structures were obtained in the presence of Ac-Lys(Ac)-D-Ala-D-Ala, a substance known to bind tightly to vancomycin. Other proteins including bovine serum albumin (BSA), casein, elastase, and chymotrypsin were found to cause no morphological and fluorescence changes in the supramolecules. The unique vancomycin-induced phase transition and fluorescence change were not observed with a biphenyl derivative having L-Ala-L-Ala moiety.