Raman spectroscopy can allow the determination of lattice dynamics, chemical composition, strain level, and some electronic properties of semiconductors, including nanowires. In this work, we make a step forward in the use of Raman spectroscopy in nanowires by investigating for the first time the most challenging type of heterostructure in nanowires (a nanoscale heterostructure with constant material composition). The heterostructure is made by small (∼20 nm) domains with hexagonal crystal phase formed in cubic nanowires. We assess the phonon properties of hexagonal Ge and, remarkably, reconstruct the relative orientation of the cubic and hexagonal domains. Furthermore, information about the band structure alignment are inferred using phonons as a probe. The general procedure that we establish can be applied to several types of heterostructures. Published in Nano Letters and selected for a cover of the issue.