Zinc phosphide (Zn3P2) is an ideal absorber candidate for solar cells thanks to its direct bandgap, earth-abundance, and optoelectronic characteristics, albeit it has been insufficiently investigated due to limitations in the fabrication of high-quality material. It is possible to overcome these factors by obtaining the material as nanostructures, e.g. via the selective area epitaxy approach, enabling additional strain relaxation mechanisms and minimizing the interface area. We demonstrate that Zn3P2 nanowires grow mostly defect-free when growth is oriented along the [100] and [110] of the crystal, which is obtained in nanoscale openings along the [110] and [010] on InP(100). We detect the presence of two stable rotated crystal domains that coexist in the structure. They are due to a change in the growth facet, which originates either from the island formation and merging in the initial stages of growth or lateral overgrowth. These domains have been visualized through 3D atomic models and confirmed with image simulations of the atomic scale electron micrographs. Density functional theory simulations describe the rotated domains' formation mechanism and demonstrate their lattice-matched epitaxial relation. In addition, the energies of the shallow states predicted closely agree with transition energies observed by experimental studies and offer a potential origin for these defect transitions. Our study represents an important step forward in the understanding of Zn3P2 and thus for the realisation of solar cells to respond to the present call for sustainable photovoltaic technology.