Isomers of [Ru-2(III,III)(3,5-DTBCat)(4)](2-) (3,5-DTBCat(2-) = 3,5 -di-tert-butylcatecholate) were successfully characterized. It is found that the isomerization from the kinetically stable cis,cis form to the thermodynamically stable trans,trans form is caused not only by heating but also by the cation exchange from Na+ to n-BU4N+, revealing that the isomerization is regulated by the specific cation-anion interactions.