We report a study of InGaN and InAlN epilayers grown on GaN/Sapphire substrates by microfocused three-dimensional X-ray Reciprocal Space Mapping (RSM). The analysis of the full volume of reciprocal space, while probing samples on the microscale with a focused X-ray beam, allows us to gain uniquely valuable information about the microstructure of III-N alloy epilayers. It is found that “seed” InGaN mosaic nanocrystallites are twisted with respect to the ensemble average and strain free. This indicates that the growth of InGaN epilayers follows the Volmer-Weber mechanism with nucleation of “seeds” on strain fields generated by the a-type dislocations which are responsible for the twist of underlying GaN mosaic blocks. In the case of InAlN epilayer formation of composition gradient was observed at the beginning of the epitaxial growth.