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Red foxes (Vulpes vulpes) have been recognized as natural reservoirs for multiple pathogens and a source of infection for domestic animals, wildlife and humans. To date, no reports are available on the Bartonella rochalimae and Hepatozoon canis infection in red foxes from China. In 2018–2022, a total of 16 red foxes were sampled in two counties and a city in Xinjiang Uygur Autonomous Region (XUAR) in northwest China. Subsequently analyzed by DNA extraction amplified by polymerase chain reaction (PCR). In the present study, based on nucleotide sequence and phylogenetic tree analyses, B. rochalimae and H. canis were molecularly identified in red foxes. Our findings provide the first molecular evidence of B. rochalimae and H. canis in red foxes from China.