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Background  Anaplasmosis and ehrlichiosis are tick-borne diseases affecting humans and livestock, particularly in tropical and subtropical regions. Animal husbandry is the main activity of people on the borders of Iran and Pakistan, with thousands of cattle crossing the border each week.    Methods  PCR and sequencing of the  16S rRNA  gene was used to determine the percentage and geographical distribution of the pathogens carried by  Hyalomma  spp. ( n  = 306) collected from 126 goats, cattle and camels in the region between November 2017 and late March 2018.    Results  In total, 1124 hard ticks including 1020  Hyalomma  spp. ticks belonging to six species ( Hyalomma anatolicum ,  Hyalomma asiaticum ,  Hyalomma marginatum ,  Hyalomma dromedarii ,  Hyalomma schulzei,  and  Hyalomma detritum ) were found on the borders of Iran and Pakistan, with  H. anatolicum  being the most prevalent tick species.  Anaplasma  spp. and/or  Ehrlichia  spp. DNA was found in 68.3% of the engorged tick specimens ( n  = 256). Sequencing of a subset (12.6%) of PCR-positive samples revealed  Anaplasma ovis ,  Anaplasma marginale , and  Ehrlichia ewingii  DNA in 81.8%, 9.1%, and 9.1% of the ticks, respectively. To our knowledge, this is the first report of  E. ewingii , an important human pathogen, in Iran.    Conclusions  Based on molecular analysis, three pathogenic Anaplasmataceae were detected in six  Hyalomma  spp. parasitizing cattle, goats and camels, confirming the presence of these pathogens along the Iran-Pakistan border.    Graphical AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04956-3.

Hyalomma spp. ticks and associated Anaplasma spp. and Ehrlichia spp. on the Iran-Pakistan border