To elucidate the conditions of formation of epigenetic graphite inclusions in natural diamond, we carried out experiments on high-temperature treatment of natural and synthetic diamond crystals containing microinclusions. The crystal annealing was performed in the CO–CO2 atmosphere at 700–1100 °C and ambient pressure for 15 min to 4 h. The starting and annealed diamond crystals were examined by optical microscopy and Raman spectroscopy. It has been established that the microinclusions begin to change at 900 °C. A temperature increase to 1000 °C induces microcracks around the microinclusions and strong stress in the diamond matrix. The microinclusions turn black and opaque as a result of the formation of amorphous carbon at the diamond–inclusion interface. At 1100 °C, ordered graphite in the form of hexagonal and rounded plates is produced in the microcracks. A hypothesis is put forward that graphitization in natural diamond proceeds by the catalytic mechanism, whereas in synthetic diamond it is the result of pyrolysis of microinclusion hydrocarbons. The obtained data on the genesis of graphite microinclusions in diamond are used to evaluate the temperature of kimberlitic melt at the final stage of formation of diamond deposits.