The Maastrichtian-Palaeogene series of the Western High Atlas and Meseta Basins in Morocco are particularly rich in palygorskite. The present work is aimed at clarifying the genesis of palygorskite from the interbedded facies and gaining an understanding of their relationships with the depositional environment. The mineralogical characteristics of palygorskite from these series were studied by X-ray diffraction (XRD) and electron microscopy (SEM/TEM). The palygorskite content and microstructure show large geographical and stratigraphical variations in the deposits studied. The palygorskite occurrence is directly related to palaeobathymetry, since it is the dominant clay mineral in shallow marine and restricted environments. According to the morphology of palygorskite crystallites, four types of textures were distinguished. These types of palygorskite are polygenetic, formed by chemical precipitation, by the recrystallization of smectite clays or reworked by wind or water from sub-aerial environments. The difference between the two studied sub-basins with respect to palygorskite occurrence is attributed to the palaeomorphology of the hinterlands, to the tectonic differentiation and to the physical-chemical conditions of seawater.