The strongest evidence for host specificity of mammalian trypanosomes comes from parasites of the subgenus Trypanosoma (Herpetosoma). Laboratory studies have shown that T. (Herpetosoma) species will not infect an alternative host. However, this has not been demonstrated in wild populations. We screened 560 bank voles (Clethrionomys glareolus) and 148 wood mice (Apodemus sylvaticus) for trypanosomes by PCR amplification of the 18S rRNA gene. In total, 109 (19%) bank voles and 12 (8%) wood mice were infected. A HaeIII restriction site was discovered that could be used to discriminate between T. (H.) evotomys of the bank vole and T. (H.) grosi of the wood mouse. All the parasites in the bank voles were identified as T. (Herpetosoma) evotomys by RFLP-PCR. Out of the 12 wood mouse infections 10 were due to T. grosi. Two of the wood mice were infected with parasites with a novel genotype that was most similar to those of T. evotomys and T. microti of voles. Fifty-six fleas collected from the rodents were also screened for trypanosomes; 9 were infected with T. evotomys and 1 with T. grosi. One of the fleas infected with T. evotomys was collected from a wood mouse.