Recently ZnO epitaxial layers have been widely studied as a semiconductor material for optoelectronic devices. Sapphire and silicon are commonly selected as substrate materials for ZnO epitaxial growth. In this communication, we report the effect of the ECR plasma pretreatment of sapphire and silicon substrates on the nucleation in the ZnO ALE (atomic layer epitaxy). It was found that ECR plasma pretreatment reduces the incubation period of the ZnO nucleation. Oxygen ECR plasma enhances ZnO nucleation most effectively since it increases the hydroxyl group density at the substrate surface. The nucleation enhancing effect of the oxygen ECR plasma treatment is stronger on the sapphire substrate than on the silicon substrate since the saturation density of the hydroxyl group is lower at the sapphire surface than that at the silicon surface.