Zinc selenide is an excellent matrix material to dope with rare-earth and transition metal to achieve mid-infrared luminescence to develop high power lasers. The luminescence, morphology and refractive index is significantly affected by the doping and defects generated due to size and valency of dopants, concentration, growth process and convection during the growth. The aim of the study is to investigate effect of point and line defects generated due to low doping of iron and chromium on the emission and morphology of the zinc selenide. Luminescence and morphological properties of large iron and chromium doped zinc selenide single crystals were studied to evaluate the effect of extremely low residual impurities and defects associated with the doping process. The emission properties following both short wavelength (i.e., ultraviolet; 350–370 nm) excitation and longer wavelength (i.e., near infrared; 850–870 nm) excitation were characterized. Luminescence emission bands were identified in both doped crystals. In addition to the primary emission bands, satellite peaks and intra-center transitions were also observed. Due to local population defects associated with the residual impurities (ppm to ppb) in the Fe-ZnSe and Cr-ZnSe crystals, peak emission wavelengths were observed to shift. The emission bands were found to decrease in intensity due to recombination of residual impurity co-dopants and complex defects generated during growth and fabrication. Cryogenic temperature analyses revealed a very clean emission band due to freezing of some of the point and line defects. An emission band observed at 980 nm for both crystals at room temperature as well as cryogenic temperatures indicates a vibronic peak in ZnSe. The scanning electron microscopy (SEM) images of the local morphology support the conclusion that small crystallites in doped crystals are also present.