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A novel, simple and generic method for the preparation of hydrophobic nanocrystal loaded composite capsules is introduced. Firstly, magnetic Fe(3)O(4) nanocrystals prepared by pyrolysis of fatty acid iron salts in non-aqueous media were successfully incorporated into water-dispersible polyglutamate/polyelectrolyte capsules by combining an ultrasonic protocol and polyelectrolyte layer-by-layer (LBL) assembly. Then, inspired by the similar synthesis mechanism of oxide and semiconductor nanocrystals based on organometallic approaches in non-aqueous media, two kinds of fluorescent semiconductor quantum dots (zinc sulfide-capped cadmium selenide nanocrystals) were chosen as models to explore QD loaded composite capsules. With rhodamine B isothiocyanate (RBITC) tagging PEI as outer layers, fluorescence micrographs and confocal microscopy images indicate that CdSe/ZnS QDs were successfully incorporated into polyglutamate/polyelectrolyte capsules with almost unchanged optical properties and the color of RBITC tagging PEI shell can be changed under different excitation. Color transformation ascribed to spectral conversion of embedded QDs was also observed after the capsules were stored under day light for days. TEM, electron diffraction (ED), and ESEM revealed that the method leads to well-defined nanocrystal loaded composite nanocapsules and is simple and generic.