We have investigated influence of substrate nitridation before growth on initial growth process of GaN heteroepitaxial layers grown on Si(0 0 1) and Si(1 1 1) substrates by electron cyclotron resonance assisted molecular-beam epitaxy. The substrate nitridation of Si(1 1 1) suppresses the inclusion of zincblende-GaN (beta -GaN) crystal grains and Facilitates the epitaxial growth of wurzite-GaN (alpha -GaN) accompanying the improvement of crystalline quality. On the other hand, the nitridation of Si(0 0 1) does not suppress the inclusion of beta -GaN and degrades crystalline quality of alpha -GaN.