Anaplasma phagocytophilum infection is a recently emerged tick-borne zoonosis. The bacterium's reservoirs likely comprise cervids, some ruminants, rodents, and perhaps other small and intermediate-size mammals; the main vector in Europe is the Ixodes ricinus tick. The Białowieza Primeval Forest is an ecosystem with a known prevalence of tick-borne pathogens. We studied the root-vole Microtus oeconomus to evaluate the natural infection of A. phagocytophilum. Intragranulocytic bacterial clusters (morulae) were not seen, but the A. phagocytophilum-specific nested polymerase chain reaction (PCR) product, targeting the rrs gene, was detected in two out of 30 rodent samples (GenBank accession nos. DQ361024 and DQ361025). Twenty-six root vole (86.6%) hosted ticks, mainly Dermacentor reticulatus larvae and nymphs. Only two rodents were parasitazed by I. ricinus single larvae. These data show the presence of natural infection of A. phagocytophilum among the root-vole M. oeconomus in the Białowieza Primeval Forest ecosystem.