The flexibility (or breathing behavior) of zinc-based metal organic frameworks (MOFs) has been manipulated by regioisomeric and positional control of organic functionalities. Ten new regioisomeric BDC (ortho- or para-disubstituted benzene-1,4-dicarboxylic acid) ligands have been synthesized and applied to a DMOF (dabco MOF) system, which has a zinc(II) paddle-wheel SBU (secondary building unit). Among the new regioisomeric MOFs, the NH2-OMe combination showed significant flexibility (breathing behavior) changes by simply altering the functional group positions (from 2,3 to 2,5). The electronic density of the benzene ring was considered to be a major factor in the flexibility changes in the regioisomeric MOF system.