Anaplasma phagocytophilum strains from different geographical regions are characterised by diverse potential infectivity for humans and domesticated animals. We investigated the potential pathogenicity of A. phagocytophilum strains in Ixodes ricinus ticks from 11 geographically different localities in Serbia. Sequences obtained in this study showed a high variability of p44 paralogues. Some of them, however, formed groups with similarities greater than 86% ('similarity groups'). Previous studies showed that 'similarity groups' were nearly always country specific. Our results correlated with this observation, and we also observed significant clustering of paralogues according to vector and reservoir origin of A. phagocytophilum strains. According to the high genetic similarity of sequences isolated from ticks collected in four localities, namely Avala, Batrovci, Hajducka cesma and Ljubovija, with paralogues with proven pathogenicity isolated from human granulocytic anaplasmosis (HGA) patients and A. phagocytophilum infected sheep, we could assume that strains with potential infectivity for humans and domestic animals were present in Serbia.