There is limited information about the genesis, classification, and properties of calcareous and gypsiferous soils of western Iran. This study investigated the morphological, physical, and mineralogical characteristics of soils on different physiographic units, including plateau, colluvial fans, and piedmont plain in the Aleshtar region. The results indicated that the parent materials (calcareous and gypsiferous) as well as topographic conditions had the most influence on the soil profile development, pedogenic processes, and clay mineralogy. Illite, chlorite, smectite, palygorskite, and kaolinite clay minerals were identified using X-ray powder diffraction, transmission electron microscopy, and scanning electron microscopy. Illite, chlorite, and kaolinite have genetically been inherited from parent rocks. Neoformation of smectite and palygorskite other than genetic inheritance was formed as a result of calcite and gypsum precipitation and poor drainage. Calcareous soils with the petrocalcic horizon and gypsiferous soils contained more pedogenic palygorskite. In conclusion, we suggest adding a new great group of Gypsixerepts to the soil taxonomy to reflect the presence of pedogenic gypsum in Inceptisols.