We report on the effects of substrate temperature and surface morphology of p-GaN templates on the properties of ZnO:Ga (GZO) layers grown by plasma-assisted molecular beam epitaxy. Substrate temperature varying from 200 °C to 450°C was found to have only a moderate effect on the electrical properties of GZO films but it greatly affects the surface morphology of the GZO films. The surface morphology and growth mode of GZO were also found to be considerably affected by the surface morphology of underlying p-GaN templates. On p-GaN templates with a smooth surface (RMS = 0.4 nm) featured by clear atomic steps, GZO layers grew in 2D growth mode and exhibited smooth surfaces with RMS roughness of 2 nm. In contrast, on p-GaN without clear atomic steps but having comparable surface roughness of 0.6 nm, GZO layers grew in 3D growth mode and exhibited rough surface (RMS roughness of ~17.0-20.0 nm). The results of surface roughness are consistent with those from TEM measurements. The lowest resistivity of ~2.3×10-4 Ω·cm for as-grown GZO layers has been achieved at substrate temperature of 350°C, while the data for 2D GZO layers was affected by a parallel conduction channel from underneath GaN and require further studies. Although the differences in electrical properties and surface morphology existed, the GZO layers grown on different p-GaN templates showed optical transparency higher than 90% in the visible spectral range. The performance of 3D GZO layers as p-electrode was tested in InGaN light emitting diodes.