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The present study proposes an important contribution to the understanding of ionic liquid role as structure directing agent for zeolite synthesis. A series of imidazolium based ionic liquids are used for this purpose. While the anionic counterpart influences the micellar organization during the synthesis, the imidazolium cation clearly directs the structure to one or another zeolite family as a function of its substituents and their interaction with the zeolite framework. The experimental observations are contrasted with molecular modeling explaining the distinct zeolite families obtained on the basis of different preferential orientation of the ionic liquids to the Si 33 precursor. [Display omitted] • The imidazolium cation clearly directs the zeolite structure to one or another family. • TON structure is observed when [Emim]+ is used as template unlike for [Bmim]+ and [Hexmim]+ where MFI was the main phase. • Computational results shown that [Emim]+ had a preferential orientation respect to the Si 33 precursor leading to TON structure. [ABSTRACT FROM AUTHOR]