In an attempt to identify the main vector and possible transmission routes of Anaplasma spp. in a region of Hungary with high prevalence of ovine and bovine anaplasmosis, DNA was extracted from 316 haematophagous arthropods (individually or in pools), including 4 species of ixodid ticks, 6 species of tabanid flies and hornflies. Midichloria-like organisms were identified with PCR (amplifying a portion of the 16S rRNA gene) and sequencing from Dermacentor marginatus and Ixodes ricinus. Significantly higher 16S positive D. marginatus individuals were collected in March than in April, suggesting earlier questing of ticks that contain rickettsial agents (thus endosymbionts). Midichloria- and Wolbachia-like organisms were also found in randomly caught horse flies (Tabanus bovinus and T. tergestinus) as well as hornflies (Haematobia irritans), respectively, with 97-99% similarity to sequences deposited in the GenBank. Although all ticks were negative in the Anaplasma spp.-specific msp4 PCR, four individuals of T. bovinus collected near to grazing cattle were positive for Anaplasma marginale. The results of the present study provide the first molecular evidence for the potential mechanical vector role of T. bovinus in the transmission of A. marginale, and broaden the range of haematophagous arthropods harbouring Midichloria-like bacteria, for the first time in any Dermacentor or Tabanus species.