SAPO-11 samples were synthesized with i-Pr2NH as a novel template, and applied in catalytic skeletal isomerization of linear butenes. More linear butenes were converted with increasing Si content in SAPO-11 samples, while the iso-butene selectivity was proportional to the Si content only in the lower reaction temperature region. The maximum yield of iso-butene was achieved around 763 K. The acidic properties of SAPO-11 samples were studied by NH3-TPD and IR spectroscopy. The strong acidity was due to the formation of Si domains in the framework lattice.