The nature of the interfacial structure between the core and the arms of a tetrapod quantum dot (QD) formed during the heteroepitaxial growth of a ZnS arm onto a CdSe core is not well understood but can be analyzed through the use of high-frequency electron paramagnetic resonance (HF-EPR) spectroscopy. The spectroscopic resolution at high frequency allows the presence of unique crystal fields reflecting interfacial alloying to be analyzed by incorporating Mn(II) ions as a dopant into the QD to act as an intentional EPR active spectroscopic probe. In addition, the HF-EPR can spectroscopically observe the presence of ion vacancies that are anticipated to form at the heteroepitaxial interface to accommodate structural mismatch. The HF-EPR spectra for Mn(II) are extremely sensitive to perturbations of the microenvironment due to changes in the crystal field. The HF-EPR spectra of Mn(II) in a CdSe (core)/ZnS (arm) tetrapod exhibiting wurtzite symmetry for both core and interface of the tetrapod provide clear evidence of heteroalloying at the core-arm interface and formation of intrinsic dislocations at grain boundaries. The formation of the interfacial alloy and grain boundaries reflects short-range ion migration at the heteroepitaxial layer to reduce strain energy due to the 12% lattice mismatch between the wurtzite lattices of CdSe and ZnS.