A simple method was established for the preparation of thio-substituted thionucleobases using room temperature ionic liquids (RTILs) such as 1-butyl-3-methylimidazolium trifluoroacetate [BMIM]+[CF3COO]−and 1-methoxyethyl-3-methylimidazolium trifluoroacetate [MeOEtMIM]+[CF3COO]−as solvents and catalysts without any other catalyst. These reactions proceeded efficiently in RTILs with excellent yield of products. RTILs can be recycled and reused effectively without further purification.