The precise placement of different materials in specific regions of a nanocrystal is important for many applications, but this remains difficult to achieve synthetically. Here we show that regioselectivity during partial cation exchange reactions of metal chalcogenide nano crystals emerges from crystallographic relationships between the precursor and product phases. By maximizing the formation of low-strain interfaces, it is possible to rationally integrate three distinct materials within uniform spherical and rod-shaped colloidal nanoparticles to produce complex asymmetric heterostructured isomers. Through sequential partial exchange of Cu+ in Cu1.8S nanocrystals with Zn2+ and Cd2+, five distinct ZnS/CdS/CuisS nanosphere and nanorod isomers are accessible.