Silica encapsulated ZnSe/ZnS quantum dots (QDs) are prepared via a sol-gel method by hydrolyzing tetraethyl orthosilicate (TEOS) on the surface of the QDs. The photoluminescence (PL) intensity of ZnS coated ZnSe QDs is more than three times that of ZnSe QDs. By partial interchange of the capping ligand from thioglycolic acid (TGA) to 3-mercaptopropyltri-methoxysilane (MPS) on the QDs, initial PL efficiency of the QDs in water was retained. The average size and morphology of the multicore-shell structured ZnSe/ZnS@SiO2 can be controlled by varying MPS and TEOS concentration.