Ticks, fleas, and vector-borne pathogens were surveyed in diverse small mammals in Yosemite National Park, California, from 2005 to 2007. A total of 450 unique captures of small mammals was collected during a 3-yr period and yielded 16 species of fleas and 10 species of ticks, including known vectors of Anaplasma phagocytophilum and Borrelia burgdorferi and plague. Serology was performed for A. phagocytophilum, spotted fever group Rickettsia spp., B. burgdorferi, and Yersinia pestis. A. phagocytophilum exposure was identified in 12.1% of all wild small mammals tested, with seropositive animals in 10 species, notably Belding's ground squirrels (Spermophilus beldingi), jumping mice (Zapus princeps), and voles (Microtus sp.). Spotted fever group Rickettsia spp. exposure was detected in 13.9% of all small mammals tested, with seropositive animals in eight species. Additionally, 37.0% of rodents in five species tested were seropositive for B. burgdorferi. No individuals were seropositive for Y. pestis. No animals were polymerase chain reaction positive for any pathogen tested. These results provide baseline data for future research and prediction of emerging vector-borne disease in Yosemite National Park, as well as adding to the known ranges and host species for tick and fleas in California.