Cu-Ni ore bodies from five Botswana mines were investigated, using a combination of X-ray diffraction, thermomagnetic measurements, Mössbauer spectroscopy, and Inductively Coupled Plasma-Atomic Absorption Electro-optic Spectroscopy (ICP-AES). The four dominant phases in the ores were found to be pyrrhotite, magnetite, pentlandite, and chalcopyrite. Mössbauer spectroscopy shows that pyrrhotite is the dominant Fe-bearing phase in the samples with 75% in B-S1, 84% in B-S2, and 80% in B-S4 and was selected for detailed characterization. Our results show that the three first techniques provide an excellent approach to estimate the degree of polytype intermixing in pyrrhotite. Accordingly, the ores can be grouped into three types: A hexagonal (or peak-type), with a 5c stacking arrangement; a monoclinic (or Weiss-type), with a 4c stacking arrangement; and a mixture of monoclinic and hexagonal types. A low-temperature study of the monoclinic form shows that the low-temperature magnetic transition close to 35 K has features similar to the Verwey transition in magnetite induced by Jahn-Teller distortion due to orbital order-disorder transition.