The intermediate nucleation layer effects on the crystal structure of GaN epitaxial layers grown on GaAs (001) substrates by solid-source molecular beam epitaxy using RF-N 2 plasma as a nitrogen source were investigated. The crystal structure of GaN grown on (001) GaAs substrates was critically influenced by the nucleation layer, that is, mainly cubic GaN was grown directly on the GaAs substrate with the epitaxial relationship of GaN (001)//GaAs(001) and GaN[110]//GaAs[110], while hexagonal GaN was grown on a very thin AlAs intermediate layer with the epitaxial relationship of GaN(0001)//GaAs(001) and GaN[1120]//GaAs[110]. X-ray diffraction and transmission-electron-microscope are used to analyze the crystal structure of the two kinds of epilayers.