Strong and stable visible-light-emitting boron nitride nanotube (BNNT)/biomolecule nanohybrids were successfully fabricated via noncovalent functionalization of BNNTs with flavin mononucleotides (FMN). Atomic force microscopy showed excellent dispersion of the nanohybrids in aqueous solution. Infrared absorption spectroscopy revealed strong π-π stacking interactions between FMN and BNNT sidewalls. Importantly, the fluorescence spectra revealed that the nanohybrids were highly fluorescent in the visible-light spectral range. Moreover, this fluorescence had unique pH-dependent and thermally stable properties. These nanohybrids might be used to construct novel fluorescence imaging probes that function over a wide pH and temperature range.