Blood samples were repeatedly collected from 12 sympatric woodland rodents over a 12-month period and DNA extracts from each were incorporated into a bartonella-specific PCR targeting a fragment of the 16S/23S rRNA intergenic spacer region (ISR). The composition of each amplicon was analysed using restriction enzyme analysis (REA) and base sequence comparison. Bartonella DNA was detected in 70 of 109 samples. Eleven samples contained DNA derived from more than one strain. Sequence analysis of 62 samples found 12 sequence variants (ISR genotypes) that were provisionally assigned to 5 different species, 2 of which were newly recognized. Up to five different species were detected in each animal. On about two-thirds of occasions, a species detected 1 month was not there the next, but never was a genotype superseded by another of the same species. However, a genotype could be re-encountered months later in the same animal, even if interim samples contained other genotypes. Our results suggest that although most animals are bacteraemic most of the time, specific infections are often superseded and that a complex and dynamic epidemiology of bartonella bacteraemias exists in woodland rodents.