CdSe/ZnS quantum dots (QDs) were incorporated into biocompatible polyisoprene particles by microencapsulation through emulsification/solvent evaporation, a technique that is facile, robust, and inexpensive. Emulsification/solvent evaporation results in QDs encapsulated into the particle core without requiring chemical modification of the as-prepared QDs. The polyisoprene can be easily crosslinked after encapsulation to enhance the fluorescence stability of the QDs. The resulting nanocomposite particles form as colloidally stable suspensions in water that exhibit stable fluorescence for months. The surface of the nanocomposite particles was functionalized with carboxylates during the QD encapsulation to facilitate subsequent bioconjugation. Streptavidin coated polyisoprene-QD particles displayed selective binding to biotin-conjugated polystyrene spheres, thus demonstrating the potential application of these particles in biolabeling.