Six species of wild rodents were sampled at 10 sites in 2002 and 2003 to determine the prevalence of Bartonella infections in rodent communities near Saskatoon, Saskatchewan, Canada. Isolates were characterized genotypically and compared with isolates found at other locations. Of 104 wild rodents examined, 57% were infected with Bartonella and prevalence within species varied from 49% for Richardson's ground squirrels (Spermophilus richardsonii) to 90% for Franklin's ground squirrels (S. franklinii). Infected rodents were found at all sites. Sequencing of a 379-bp portion of the citrate synthase gene was performed on 54 isolates and revealed 13 distinct genotypes, eight of which had not been described previously. The most common genotype detected in red-backed voles (Clethrionomys gapperi) was 99.1% similar to B. grahamii, a known human pathogen. Two of 10 Franklin's ground squirrels were concurrently infected with multiple Bartonella genotypes. All genotypes, with the exception of one detected in both Franklin's and thirteen-lined ground squirrels (S. tridecemlineatus), were found in only one host, and all genotypes from each species, with the exception of genotypes detected in red-backed voles, clustered together within the same relatedness group, suggesting that at least some Bartonella genotypes are specific to some rodent hosts.