Transmission electron microscope (TEM) and transmission electron diffraction (TED) examination has been performed to investigate microstructural properties of gas source molecular beam epitaxial GaN(As,P) layers grown on (0001) GaN/sapphire at temperatures in the range 500–760 °C. As for the GaNAs, we report the observation of ordering with a space group P3ml in the layer grown at 730 °C. The layers grown at temperatures below 600 °C are polycrystalline, whist the 730°C GaNAs layer has epitaxial relation to the GaN substrate. It is also shown that the GaNAs layers experience a structural change from a zinc-blende phase to a wurtzite phase, as the growth temperature increases. As for the GaNP, it is shown that the layers grown at temperatures ≤ 600 °C experience phase separation resulting in a mixture of GaN-rich and GaP-rich GaNP with zinc-blende structure. However, the layers grown at temperatures ≥ 730 °C are found to be binary zinc-blende GaN(P) single crystalline materials. The layers grown at temperatures ≥ 730 °C consist of two types of micro-domains, i.e., GaN(P)1 and GaN(P)11; the former having twin relation to the latter.