Isothermal annealing of two partially metamict zircon from Sri Lanka were carried out at 870 K, 968 K, 1071 K, and 1166 K for 0.5 min up to ∼; 210 hours. Raman spectroscopy was used to monitor the amorphous-to-crystalline transformation. The evolution of the phonon frequency and the linewidth of the v3 Si-O stretching band in zircon with annealing time clearly shows two recovery stages within the temperature and time ranges of the experiments. Both annealing stages form distinct linear segments in the frequency vs. linewidth plot, which are clearly separated from the trend defined by untreated metamict zircons. The first stage is characterized by the recovery of the short-range order, i.e. by the recovery of pre-existing, disordered crystalline domains as indicated by a fast recovery rate of the phonon frequency at the beginning of the transformation. This process dominates at temperature below ∼; 1000 K. In the case of the less metamict zircon, first stage recovery was activated after significant incubation periods, which follow an Arrhenius relationship. The second stage involves epitaxial recrystallization, which is activated within the first few minutes at temperatures > 1000 K (e.g., after ∼ 1–2 min at 1166 K). At this stage, the decrease of the linewidth is most probably related to the relaxation of phonon confinement associated with the growth of crystalline domains. We have estimated empirical activation energies of EA = 2.24 ± 0.04 eV and EA = 2.6 ± 0.2 eV for the first stage from the isothermal frequency and linewidth transformation curves. These activation energies are most likely related to recombination of point defects in the crystalline domains of partially metamict zircon. A single activation energy of EA = 3.8 ± 0.4 eV was obtained for epitaxial recrystallization by assuming Johnson-Mehl-Avrami growth kinetics as a first approximation. We suggest that a comparison of frequency versus linewidth relationships observed for natural zircons with experimental trends provides a potential means for recognizing an annealing history of natural zircons, provided that post-annealing radiation damage did not completely obscure the annealing effect.