A novel approach for selectively encapsulating Cy5 dye molecules via DNA hybridization in cationic phosphorus dendrimers (G(4)(+))/polystyrenesulfonate (PSS) microcapsules has been developed. The hybridization between Cy5 labeled single strand DNA (ssDNA) targets and complementary ssDNA probes was performed in the microcapsules. During hybridization, the ssDNA targets acted as 'vehicles' and Cy5 dye molecules as 'cargos', which led to the selective encapsulation of the Cy5 molecules inside the capsules. The approach may be applied for many small molecules, which are usually difficult to be encapsulated due to their diffusion properties in microcapsules.