Silica "nanobubbles" are hollow spheres of silica that can be used as nanometer-sized containers for probe molecules. A method for the encapsulation of a fluorescent molecule into silica "nanobubbles" is reported. Fluorescein isothiocyanate (FITC) dye molecules were coadsorbed onto the surface of gold nanoparticles with 3-aminopropyltrimethoxysilane. Following silica condensation, and dissolution of the gold core, the fluorescent molecules remain inside the water-filled, but sealed, silica nanoparticle. The plasmon band of the gold particles and the absorption and fluorescence spectra of the dye are affected by adsorption of the molecule on the gold particle. Encapsulation in the silica nanobubble insulates the dye molecule from the external environment. Analogous methods can be applied to a wide range of probes.