Effects due to phase separation in InGaN have been identified as having major effects on the performance of devices, in particular light-emitting diodes (LEDs) and injection lasers. However, the complexity of the various materials phenomena that can occur has led to a great deal of recent confusion. Much of this confusion can be eliminated by considering the experimentally measured materials properties in the context of the set of physical phenomena occurring during epitaxial growth, including coupling that exists between the various effects. Spinodal decomposition is expected to produce phase separation due to the miscibility gap in InGaN alloys. However, the actual occurrence of this phenomenon has been disputed due to the complexity of real systems. For example, the region of solid immiscibility for InGaN is strongly dependent on elastic strain. In addition, the strain, itself, affects properties such as the bandgap energy. Complicating the analysis of these phenomena is that the solid composition can be affected by elastic strain due to the well-known thermodynamic phenomenon of “compositional pulling”. An additional factor must be considered if the experimentally observed phenomena are to be understood. Thin, lattice mismatched epitaxial layers are coherent with the substrate (or underlying layer). Thus, the actual growth process for the formation of lattice mismatched layers, namely the Stranski–Krastanov (S–K) formation of islands, must be included in any realistic growth model. By considering all the phenomena together, including the coupling between them, it becomes clear that several separate mechanisms exist for phase separation. The focus of this paper is the analysis of the thin (2–3 nm), coherent InGaN layers used in the quantum well structures used for virtually all LEDs and lasers produced by the S–K mechanism. By considering these coupled phenomena together it is possible to arrive at a coherent interpretation of the various materials properties measured using techniques such as high resolution transmission electron microscopy, X-ray diffraction, and optical techniques as well as the device characteristics.