The present work deals with the synthesis of crystalline carbon nitride thin films by microwave plasma assisted chemical vapour deposition in N$_2$/CH$_4$ gas mixture. The discharge analysis by optical emission spectroscopy shows that the increase in the N$_2$/CH$_4$ ratio involves an important production of the CN and C$_2$ radicals. In the films X-ray energy dispersion spectroscopy shows that the N/C ratio decreases when the CH$_4$ percentage in N$_2$ increases. Xray diffraction and electron diffraction are used to study the carbon nitride films nature. Scanning electron microscopy shows that the films consisted of nano-crystalline grains. Carbon balls are also present on the film surface for CH$_4$ percentage higher than 4%. The transmission electron microscopy confirms the nano-structure of the film and shows the isotropic etching of the substrates, during the film growth.