The morphology of thin InGaN layers grown on c-plane GaN substrates by metalorganic vapor phase epitaxy (MOVPE) has been studied by atomic force microscopy. Three different morphologies appeared, a stepped surface, large flat two-dimensional (2D) islands and small high three-dimensional (3D) dots. Low growth temperature and high growth rate (i.e. increased vapor supersaturation) changed the InGaN morphology from steps to 2D islands and then 3D dots (when exceeding the critical thickness for 3D dots). Larger miscut angle of GaN substrate changed the morphology from 2D islands to step by decreasing the surface supersaturation of individual terraces. InGaN layers with a stepped morphology had the highest internal quantum efficiency at similar InN mole fraction. InGaN grown on GaN substrate more easily achieved a stepped morphology compared to InGaN on GaN/sapphire templates.