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Crystallization of SAPO-5 and SAPO-34 molecular sieves with microwave and conventional electric heating of the same gel has been investigated in an alkaline condition using N,N,N’,N’-tetraethylethylenediamine as a template molecule. SAPO-5 structure can be selectively prepared with microwave heating because of the fast crystallization of the technique. On the other hand, SAPO-34 is the sole product with usual conventional electric heating because SAPO-5 can be gradually transformed into SAPO-34 structure with an increase in crystallization time. This phase selectivity is probably because of the relative stability of the two phases at the reaction conditions (kinetic effect). Crystallization with microwave heating can be suggested as a phase selective synthesis method for relatively unstable materials because of fast crystallization.