The role of the acid site location in H-ferrierite (H-FER) on the skeletal isomerization of linear butenes was studied. Assignment of OH groups observed in FTIR analysis is addressed taking into account previous NMR and computational studies regarding the FER structure. Possible locations of alkali ions in the zeolite framework are discussed. Close structure activity relationship has been observed between Bronsted acid sites located in the 10 member ring (MR) channels and selective isobutene formation, Molecular dynamics (MD) calculations of possible products observed during n-butene transformation at reaction temperatures support the experimental findings.