Rodents are important reservoir hosts of many tick-borne pathogens. The aim of this study was to identify the presence of Anaplasma phagocytophilum, Candidatus Neoehrlichia mikurensis and protozoan parasites of Apicomplexa family and to study their ecologic associations. Genetic variability of A. phagocytophilum was studied by DNA sequencing followed by phylogenetic analyses of loci. The bacteria were detected in questing I. ricinus ticks (0.7%) from all studied sites, as well as from feeding I. trianguliceps (8.9%) on rodents. In areas where I. trianguliceps ticks were absent we did not detect A. phagocytophilum in rodents. A. phagocytophilum was also detected in spleens (1.7%) and ear biopsies (1.4%) of rodents. Phylogenetic analysis based on genetic four loci have shown the presence of two clades. First clade contained A. phagocytophilum genotypes from questing I. ricinus and feeding I. ricinus from humans, ungulates, birds and dogs. Second clade was formed with genotypes found in rodents and feeding I. trianguliceps. We have confirmed that A. phagocytophilum strains have specific associations with two vectors and different reservoir hosts. A. phagocytophilum genotypes that are associated with rodents are probably transmitted solely by I. trianguliceps ticks, therefore these strains may not be of risk for humans. Candidatus N. mikurensis was detected in questing I. ricinus ticks (2.5%), feeding I. ricinus (0.3%) and I. trianguliceps (2.7%) ticks, as well as in spleen of rodents (1.6%). The sequences of two loci of Candidatus N. mikurensis obtained in this study confirmed high degree of homology. DNA of Babesia microti was found in biopsies of rodents (1.5%), feeding (5.1%) and questing I. ricinus ticks (0.4%). None of the 109 I. trianguliceps ticks was infected with B. microti. BLAST analysis of B. microti nucleotide sequences confirmed the presence of two genotypes, „Jena" (92%) and „Munich" (8%) strains. Results of our study confirmed the importance of rodents in the circulation of both emerging pathogens in the natural foci. This implies potential threat for humans. Since rodents are reservoir hosts of many other zoonotic and tick borne agents the ability to infect feeding ticks with two or even more pathogens is possible.