Ectoparasitic arthropods are often vectors of rickettsiosis. We conducted a survey of ectoparasites on U.S. military facilities throughout Japan with the use of specimens submitted by pest control, public health, and veterinary personnel. Over 1,600 individual ectoparasites were collected. Fifteen species were identified, including several significant vectors of human diseases such as scrub typhus and rickettsial spotted fevers. These ectoparasites included Ctenocephalides felis, Haemaphysalis longicornis, Ixodes persulcatus, Leptotrombidium fuji, Leptotrombidium pallidum, and Rhipicephalus sanguineus. Rickettsial agents were detected by PCR and DNA sequencing. These included Bartonella henselae, Bartonella japonica, a novel Bartonella, Coxiella burnetii, an unnamed Coxiella, Ehrlichia canis, Orientia tsutsugamushi, Rickettsia typhi, and “Rickettsia Rf2125”/“Rickettsia cf1and5”.