In this study, a new genetic interpretation of the Mg-bentonite deposits from the Tajo Basin is given through a high-resolution transmission electron microscopy study. These bentonites, belonging to the Green Clays and Pink Clays lithostratigraphic units, are afforded by the sum of processes occurring during the weathering of parent rocks and the evolution of the materials by the transformation of phyllosilicates in the sedimentary environment. The primary phyllosilicates progressively change their microstructure and crystal chemistry, resulting in very complex clay minerals assemblages. The Green Clays are relatively enriched in Al, Fe, and K, whereas Pink Clays are enriched in Mg and Si, corresponding to almost pure trioctahedral smectites. Although the point analysis of the particles showed a continuous compositional variation that evidences their genetical relationship, they were statistically classified in groups that represented the evolution from the primary phyllosilicates (dioctahedral and trioctahedral micas and chlorites) to the final products comprise very low-charge saponite and scarce sepiolite. The intermediate steps in this transformation included the following: 1) particles of structural formulas with an excess of octahedral cations that were interpreted as hydroxy-interlayer minerals and 2) random mixed-layers of illite/smectite progressively poorer in illitic component as the more evolved particles. Green Clays correspond to the state of transformation to smectites where partially transformed detrital components were still predominant, corresponding to more proximal facies, whereas Pink Clays represented most evolved stages in the mineral transformation. The alternation of Green and Pink Clay levels was related to climatic changes with alternation of wetter and drier periods.