We report on the selective-area heteroepitaxy and facet evolution of submicron GaN islands on GaN-sapphire, AlN-sapphire, and bare sapphire substrates. It is shown that strain due to the lattice mismatch between GaN and the underlying substrate has a significant influence on the final morphology and faceting of submicron islands. Under identical metalorganic chemical vapor deposition growth parameters, islands with low or no mismatch strain exhibit pyramidal morphologies, while highly strained islands evolve into prismatic shapes. Furthermore, islands grown with relatively low compressive mismatch strain yield more uniform arrays of pyramids as compared to the nonstrained, homoepitaxially grown crystals. It is proposed that the strain dependency of Ehrlich-Schwoebel barriers across different crystallographic planes could potentially account for the observed morphologies during selective area growth of GaN islands.