A facile method has been developed to prepare aqueous dispersions of encapsulated conjugated polymer nanoparticles exhibiting high fluorescence brightness. Salient features of the nanoparticles include their small diameter and spherical morphology. Encapsulation of the nanoparticles with a silica shell reduces the rate of photooxidation and allows facile attachment of functional groups for subsequent bioconjugation and nanoparticle assembly. Functionalization of the nanoparticle with amine groups followed by the addition of An nanoparticles resulted in the formation of nanoparticle assemblies, as evidenced by the efficient quenching of the conjugated polymer fluorescence by the Au nanoparticles.