Rodents are known to be reservoir hosts for at least 60 zoonotic diseases and are known to play an important role in their transmission and spread in different ways. We sampled different rodent communities within and around human settlements in Northern Senegal, an area subjected to major environmental transformations associated with global changes. Herein, we conducted an epidemiological study on their bacterial communities. One hundred and seventy-one (171) invasive and native rodents were captured, 50 from outdoor trapping sites and 121 rodents from indoor habitats, consisting of five species. The DNA of thirteen pathogens was successfully screened on the rodents' spleens. We found: 2.3% of spleens positive to <i>Piroplasmida</i> and amplified one which gave a potentially new species <i>Candidatus</i> "<i>Theileria senegalensis</i>"; 9.35% of <i>Bartonella</i> spp. and amplified 10, giving three genotypes; 3.5% of filariasis species; 18.12% of <i>Anaplasmataceae</i> species and amplified only 5, giving a new potential species <i>Candidatus</i> "<i>Ehrlichia senegalensis</i>"; 2.33% of <i>Hepatozoon</i> spp.; 3.5% of <i>Kinetoplastidae</i> spp.; and 15.2% of <i>Borrelia</i> spp. and amplified 8 belonging all to <i>Borrelia crocidurae.</i> Some of the species of pathogens carried by the rodents of our studied area may be unknown because most of those we have identified are new species. In one bacterial taxon, <i>Anaplasma</i>, a positive correlation between host body mass and infection was found. Overall, male and invasive rodents appeared less infected than female and native ones, respectively.