ABSTRACT: Pathogen introduction by invasive species has been speculated to be a cause of declining western pond turtle Emys marmorata populations in California, USA. This study determined the prevalence of Ranavirus spp., Herpesvirus spp., Mycoplasma spp. (via polymerase chain reaction of blood and nasal flush contents), and Salmonella spp. infection (via fecal culture) in native E. marmorata and invasive red-eared sliders Trachemys scripta elegans and compared infection prevalence in E. marmorata populations sympatric with T. scripta elegans to E. marmorata populations that were not sympatric by sampling 145 E. marmorata and 33 T. scripta elegans at 10 study sites throughout California. Mycoplasma spp. were detected in both species: prevalence in E. marmorata was 7.8% in the northern, 9.8% in the central, and 23.3% in the southern California regions. In T. scripta elegans, Mycoplasma spp. were not detected in the northern California region but were detected at 4.5 and 14.3% in the central and southern regions, respectively. All turtles tested negative for Herpesvirus spp. and Ranavirus spp. Enteric bacteria but not Salmonella spp. were isolated from feces. E. marmorata populations that were sympatric with T. scripta elegans did not have increased risk of Mycoplasma spp. infection. For E. marmorata, there was a significant association between Mycoplasma spp. infection and lower body weight and being located in the southern California region. This study is the first of its kind to document pathogen prevalence in native E. marmorata habitats and those sympatric with T. scripta elegans in California.