We investigated the adaptive evolution of gastroenteritis viruses under the repeated disinfection with free chlorine. Murine norovirus (MNV) and Rhesus rotavirus (RRV) were used as surrogates for human norovirus and rotavirus. As a result, resistant populations of these viruses to free chlorine were successfully acquired by the repeated treatment with free chlorine. The single nucleotide polymorphisms revealed that specific mutations were found in outer capsid proteins of these viruses, which implied that some mutations in structural proteins may contribute to the virion stability and lead to the change in free chlorine susceptibility. Based on these results, it was concluded that the free chlorine disinfection can be regarded as a selection pressure on gastroenteritis viruses.