H/D exchange is achieved at allylic positions of alkenes using D2O in acetone and alkene isomerization catalyst 1, which features a bifunctional imidazolylphosphine. The basic nitrogen of the latter is thought to deprotonate an alkene substrate coordinated to the CpRu center; at this stage the protonated nitrogen could undergo H/D exchange with deuterium oxide. An exceptional degree of deuteration is achieved at positions accessible to isomerization, with a high degree of control. Using biphasic settings one can literally wash out reactive protons on the substrate without using organic solvents.