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Free-ranging mule deer (MD; Odocoileus hemionus) from Arizona and California were tested for evidence of infection with several tick-borne pathogens, including species of Ehrlichia, Anaplasma, Babesia, and Borrelia. Of 125 mule deer tested from Arizona, 29 (23%) and 11 (9%) had antibodies reactive to E. chaffeensis and A. phagocytophilum by indirect immunofluorescent antibody testing, respectively; none of the six MD tested from California were seropositive. Using a commercial competitive ELISA kit, antibodies reactive to Anaplasma spp. were detected in 19 (15%) MD from Arizona and four of six (67%) MD from California. Polymerase chain reaction (PCR) testing for tick-borne pathogens was conducted on blood samples from 29 MD from Arizona and 11 MD from California. Twenty-two of 29 (75.9%) MD from Arizona had PCR evidence of infection with at least one tick-borne pathogen. We detected an Anaplasma sp. in 19 of 29 (65.5%) MD and a Babesia sp. in 10 of 29 (34%) MD. Sequencing of these amplicons indicated that the Anaplasma sp. was the same that had previously been detected in MD from California and the Babesia sp. was similar to one previously detected in a reindeer (Rangifer tarandus tarandus) from California. All of the California MD had evidence of infection with a tick-borne pathogen. Two different species of Anaplasma spp. were detected in MD from California, eight of of 11 MD were infected with an Anaplasma sp., and three of 11 MD were infected with A. ovis. This is the first report of a mule deer naturally infected with A. ovis. Ten of 11 MD from California were infected with a Babesia-like organism previously associated with human disease, and a single MD was PCR positive for Borrelia coriaceae, which has been associated with epizootic bovine abortion. Together, these data suggest that MD in northern Arizona and eastern California are exposed to several pathogens of human and veterinary importance.