Zinc selenide nanocrystals (NCs) were successfully synthesized in silicon dioxide (silica grown on a silicon wafer) by high-fluence implantation of Zn+ and Se+ ions with subsequent rapid thermal annealing at 1000°C for 3 min. The high crystalline quality of the zinc blende ZnSe nanoclusters was proven by transmission electron microscopy with selected area electron diffraction and Raman spectroscopy. Low-temperature photoluminescence (PL) reveals the recombination of excitons in ZnSe, what further indicates a good crystalline quality of the synthesized nanocrystals. PL analysis shows a strong coupling of phonons and excitons. The Huang−Rhys parameter of the longitudinal optical phonon in the exciton transition S is in the range of 0.6−0.7. Despite the excellent quality of the ZnSe NCs synthesized in silica, defect states inside the NCs or at the NCs/SiO2 interface with activation energies of 0.1–0.2, 0.45 and 0.67 eV play a crucial role in radiative recombination.