The genetic diversity of Bartonella species within a small mammal community and in individual cotton rats (Sigmodon hispidus) was examined by trapping, capturing, sampling, and releasing of marked animals over a 17-month interval. Based on sequence analyses of the Bartonella gltA gene, amplicons separated into four genogroups (A, B, C, and Pin) containing 11 variants. Although the prevalence of bacteremia due to different genogroups/variants of Bartonella was temporally variable, variants of genogroup A predominated during each sampling period. Multiple gltA variants were often (20.5% of individuals) isolated from a single cotton rat blood sample; a maximum of five variants was recovered from an individual during its sampling history. Among 92 cotton rats bacteremic at two or more sampling dates, 34 rats retained a single genetic variant, alone or in mixed infection, throughout their sampling history. The temporal course of individual infections was complex as the succession of gltA variants was variable and detectable bacteremia was often intermittent. No antibodies (titer of >1:8) were detected to homologous strains of Bartonella recovered from individual cotton rats during their sampling history. The temporal course of Bartonella infections could result from a single, persistent, and potentially multi-genogroup/variant infection, during which variants differentially dominate the detectable bacteremia.