The type of anion (fluoride, chloride, and sulfate) used in the synthesis cation exchange process of the FSM-16 mesoporous material modified its thermal stability. Compared with chloride and sulfate anions, the presence of fluoride anions gave rise to an increase of the wall thickness, which explains the higher thermal stability of this material. The fluoride anions also promote the formation of a more hydrophobic solid. The hydroxyl groups of this material, with a lesser population density than that present on the solids obtained with chloride and sulfate anions, were more active in H-D isotopic exchange with deuterium at 573 K.