Samples of MAPO-36 (ATS structure) and MAPO-5 (AFI structure) prepared with different magnesium contents and high crystallinity were characterized by several physical chemical techniques and catalytically evaluated using the isomerization of m-xylene as a reaction model. Chemical analysis of the solids indicated a greater incorporation of Mg into MAPO-5 than into MAPO-36 for the same Mg content in the gel. X-ray photoelectron spectroscopy results indicated that in both MAPOs the concentration of Mg at the surface is larger than that in the bulk in the as-synthesized samples, and that during the calcination process a depletion of the surface Mg has taken place. The calcination process of these samples caused Mg extraction from the framework of both materials. Infrared spectroscopy investigations of adsorbed pyridine showed that the acid strength of MAPO-36 is higher than that of MAPO-5, and that a high fraction of the acid sites disappears on calcining the samples in air. Temperature-programmed desorption of ammonia indicated the presence of two kinds of acid sites, the major part being strong acid sites which increase with Mg content. The catalytic activity of MAPO-36 decreases with the Mg content, which is attributed to a crystal size effect. The activity is much higher than that of MAPO-5 when the concentration of Mg in the crystals is small, but the difference decreases as the solids become richer in Mg.