Skeletal isomerization of I-pentene was carried out over SAPO and CoAPO molecular sieves with AEL and AFI type structure and for comparison over AlPO-11 and HZSM-5. The equilibrium distribution within the linear pentenes and iso-pentenes was established over all catalysts except at very low temperatures or conversions. The approach to the equilibrium distribution between the Linear pentenes and iso-pentenes depends on the strength of the acid sites, the pore dimensions and the structure of the catalyst. Over AlPO4-11, a material with very weak acid sites, the selectivity to skeletal isomerization was only 5%, while the double bond isomerization and the isomerization via methyl shift were in equilibrium. Over SAPO-11 and CoAPO-11, having medium strong acid sites and one-dimensional pores with a 10-membered ring-system, the distribution of linear and iso-pentenes was near the equilibrium. On SAPO-5 and CoAPO-5, materials with sites of similar strength and one-dimensional pores with a 12-membered ring-system, the equilibrium distribution was not achieved because of the rapid deactivation that diminished the accessibility of the acid sites inside the pores. Due to the presence of strong acid sites and a two-dimensional pore system with a 10-membered ring-system, the equilibrium distribution is achieved on HZSM-5, but this 'pentene pool' react further by dimerization and cracking.