The purpose of this study was to assess the prevalence of zoonotic bacteria, including Coxiella burnetii, Bartonella spp., Rickettsia spp., Brucella spp., Borrelia spp., and Ehrlichia spp., among small mammalian in Iran. We examined 618 small mammals collected between 2016 and 2020 from different parts of Iran. We extracted DNA from spleen samples and used quantitative real-time PCR to identify specific genes. We found 559 (90.45%) samples infected with at least one of the analyzed pathogens. Among the studied specimens, 86.08% tested positive for Bartonella spp., 2.42% for Ehrlichia spp., 0.80% for Borrelia spp., 0.64% for C. burnetii, 0.48% for Brucella spp., and 0% for Rickettsia spp. Bartonella krasnovii (25.81%) and Bartonella taylorii (25.81%) were the most prevalent among the Bartonella species. This study identified a rodent infected with Brucella abortus. Among the Borrelia-positive samples, four out of five were identified as Borrelia duttonii. Among the positive cases in the Ehrlichia genus, Ehrlichia canis, Candidatus Ehrlichia shimanensis, and Neoehrlichia mikurensis were identified. Meriones persicus was the most prevalent captured rodent with 315 specimens (51.22%). Our study revealed that a large proportion of the small mammals analyzed were infected with one or more of the targeted pathogens. M. persicus exhibited significant infection rates with C. burnetii, Bartonella spp., Ehrlichia spp., Brucella spp., and Borrelia spp. This suggests that this rodent species could serve as a crucial reservoir for zoonotic pathogens in Iran.