Since the decoding of the human genome, the need to obtain more and more molecular information from smaller and smaller samples is intensifying. Biosystem analysis, disease diagnosis, and biomedical studies all require the tracking of spatiotemporal information from multiple targets, involving proteins, genes, lipids, and glycans for target pattern recognition and system defi nition. Multiplexed assays are therefore required in order to complement advances in genomics and proteomics, and to allow a large number of nucleic acids and proteins to be rapidly screened. [1][2][3][4] Optical encoding technologies achieved by multiplexing colors and fl uorescence intensities of fl uorophores have become an attractive strategy because a large number of high-brightness probes can be readily produced. Both fl uorescent-dye- [5][6][7][8][9][10] and quantum-dot-embedded [11][12][13][14][15][16][17][18][19][20][21] multi plexed microspheres offer advantages such as fl exibility in target selection, fast binding kinetics, and well-controlled binding conditions. Unfortunately, because of the large size (typically 1-15 ΞΌ m in diameter), quenching, and relatively broad wavelength spectral response, these multicolor microspheres have limitations for applications such as gene, protein, and cell system labeling. Toward the development of uniform nanobarcode materials in the nanometer regime, a few successful attempts have been made. The most common reaction schemes include encapsulation of fl uorescent dyes and quantum dots in silica nanobeads, [ 5 , 7 , 22 ] hydrogels, [ 23 ] and surfactant micelles. [ 24 ] For dye-doped nanobarcodes, [ 5 , 7 ] measurements of intensities and their ratios are inherently diffi cult, which limits the number of levels at which a dye can be incorporated to give distinguishable beads. If the dyes have different excitation