CdSe/ZnS quantum dots (QDs) were incorporated into polyisoprene (PI) particles by microencapsulation through emulsification/solvent evaporation, a technique that is facile, robust, and inexpensive. The resulting fluorescent nanocomposite particles form as colloidally stable suspensions in water, and the PI can be easily chemically crosslinked after QD incorporation. The PI/QD nanocomposite particles were further functionalized with streptavidin, resulting in selective binding to biotin-conjugated polystyrene spheres. Methods of QD encapsulation based upon emulsification/solvent evaporation avoid the possibility of primarily surface-adsorbed QDs, yielding QDs encapsulated into the particle core. The PI/QD nanocomposites particles exhibit stable fluorescence for at least one year, and multicolor emission was demonstrated by encapsulating mixtures of different sized QDs. The nanocomposite particles offer promise as optically active tags or labels in combinatorial studies.