Babesia venatorum, formerly known as Babesia sp. EU1, is a zoonotic hemoprotozoan parasites that commonly infects deer. In the present study, we investigated B. venatorum infection in Ixodes persulcatus, an important tick vector capable of transmitting several tick-borne pathogens that cause babesiosis, encephalitis, tularemia, and Lyme diseases. DNA samples extracted from questing I. persulcatus ticks (n= 63) that had been collected in Selenge province of Mongolia in 2012 and 2013 were screened for B. venatorum using a nested PCR assay. The findings showed that two of 63 DNA samples were positive for B. venatorum. The 18S rRNA sequences amplified from B. venatorum-positive DNA samples shared high identity scores (96.1–99.9%) with known B. venatorum sequences derived from human and tick isolates. In phylogenetic analysis, the Mongolian 18S rRNA sequences clustered with the previously characterized B. venatorum sequences. In addition to reporting B. venatorum in Mongolia for the first time, the present study identifies I. persulcatus as a potential vector of this zoonotic Babesia in Mongolia. Additional studies to investigate the prevalence of B. venatorum in deer, humans, and ticks in different geographical regions are essential to understand the epidemiology of this parasite species in Mongolia.