The aim of this study was to conduct a comparative analysis of the 16S rRNA gene fragment nucleotide sequences for Anaplasma phagocytophilum strains detected in the blood of horses from various parts of Europe. The study comprised 234 horses that had had contact with ticks. Using PCR, the genetic material of A. phagocytophilum was identified in the blood of 42 animals. The sequences of the 16S RNA gene amplicons that were obtained from our A. phagocytophilum isolates had 100 % similarity with each other and 96.4-100 % similarity with Anaplasma spp. sequences selected from those available in GenBank. Nucleotide substitutions at positions 248 and 249 were demonstrated in all the 16S RNA gene sequences of Anaplasma obtained in our study. This may indicate the emergence of a new rickettsial genotype that is the cause of equine granulocytic anaplasmosis in southern and eastern Europe. These results add new information on the epidemiology and genetic diversity of A. phagocytophilum detected in the blood of horses from southern and eastern Europe.