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Clay dehydration at great depth generates fluids and overpressures in organic-rich sediments that can release isotopically light boron from mature organic matter, producing 10B-rich fluids. The B can be incorporated into the tetrahedral sites of authigenic illite during the illitization of smectite. Therefore, the crystal-chemical and geochemical characterization of illite, smectite or interlayered illite–smectite clay minerals can be an indicator of depth (temperature) and reactions with the basin fluids. The aim of this study was to determine the detailed clay mineralogy, B-content and isotopic composition in illite–smectite rich samples of mud volcanoes from the Gulf of Cádiz, in order to evaluate interactions of hydrocarbon-rich fluids with clays. Molecular modeling of the illite structure was performed, using electron density functional theory (DFT) methods to examine the phenomenon of B incorporation into illite at the atomic level. We found that it is energetically preferable for B to reside in the tetrahedral sites replacing Si atoms than in the interlayer of expandable clays. The B abundances in this study are high and consistent with previous results of B data on interstitial fluids, suggesting that hydrocarbon-related fluids approaching temperatures of methane generation (150 °C) are the likely source of B-rich illite in the studied samples.