Naphthoimidazolium groups can form unique ionic hydrogen bonds with anions as imidazolium moieties, and in addition, they are fluorescent, so no further elaborative synthesis is needed to introduce a fluorescent group. In this paper, three naphthoimidazolium derivatives were synthesized and studied for the recognition of nucleotides. Compound 1 composed of a single naphthoimidazolium group and quaternary ammonium group did not show any significant fluorescent changes with various anions and nucleotides, such as ATP, GTP, CTP, TTP, UTP, ADP and AMP. A tripodal compound 3 bearing three naphthoimidazolium groups and three quaternary ammonium groups, respectively, showed large fluorescence enhancements with UTP, CTP and TTP and moderate fluorescence enhancements with ATP and pyrophosphate and a fluorescence quenching effect with GTP. On the other hand, compound 2 bearing two naphthoimidazolium groups and two quaternary ammonium groups displayed a selective fluorescence enhancement with ATP and a selective fluorescence quenching effect with GTP in 100% aqueous solution.