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 Si33 precursor.