Zinc germanium diphosphide (ZnGeP2) is a ternary semiconductor best known for its nonlinear optical properties. A primary application is optical parametric oscillators operating in the mid-infrared region. Controlled donor doping provides a method to minimize the acceptor-related absorption bands that limit the output power of these devices. In the present study, a ZnGeP2 crystal is doped with selenium during growth. Selenium substitutes for phosphorus and serves as a deep donor. Significant concentrations of native defects (zinc vacancies, germanium-on-zinc antisites, and phosphorous vacancies) are also present in the crystal. Electron paramagnetic resonance (EPR) is used to establish the atomic-level model for the neutral charge state of the selenium donor. The S = 1/2 signal from the neutral donors is produced at 6 K by illuminating with 633 nm light (electrons excited from doubly ionized Zn vacancies convert SeP+ donors to SeP0 donors). A g matrix, with principal values of 2.088, 2.203, and 1.904, is extracted from the angular dependence of the EPR spectrum. The principal-axis direction associated with the 1.904 principal value is close to a Se–Ge bond. This indicates an asymmetric distribution of unpaired spin density around the selenium ion and thus predicts the deep donor behavior.