The influence of synthesis parameters (e.g. Si/Al ratio, pH of the reaction mixture, structure of Gemini-type surfactant) on the phase selectivity of nanocrystalline MOR formation was studied. The nature of organic structure-directing cation (i.e. charge, size) was found as a decisive factor controlling morphology of MOR nanocrystals. Fabricated nanocrystalline MOR zeolites showed enhanced textural characteristics (BET area, total pore volume) and higher catalytic activity (TOF = 42-45 vs. 15 h(-1)) in acid-catalyzed annulation reaction of 2-naphtol with methylbut-3-en-2-ol when compared to commercial microcrystalline MOR zeolite.