Heteroepitaxy of SiGe alloys on Si (001) under certain growth conditions has previously been shown to cause self-assembly of nanostructures called Quantum Dot Molecules, QDMs, where pyramidal pits and 3D islands cooperatively form. QDMs have potential applications to nanologic device architectures such as Quantum Cellular Automata that relies on localization of charges inside islands to create bi-stable logic states. In order to determine the applicability of QDMs to such structures it is necessary to understand the nano-scale chemistry of QDMs because the chemistry affects local bandgap which in turn affects a QDM's charge confinement property. We investigate the nanoscale chemistry of QDMs in the Si0.7Ge0.3/Si (100) system using Auger Electron Spectroscopy (AES). Our AES analysis indicates that compressively strained QDM pit bases are the most Ge rich regions in a QDM. The segregation of Ge to these locations cannot be explained by strain energy minimization.