Coxiella burnetii, a zoonotic bacterium, has recently been identified in several marine mammal species on the Pacific Coast of North America, but little is known about the epidemiology, transmission, and pathogenesis in these species. We tested sera archived from northern fur seals (NFS, Callorhinus ursinus; n=236) and Steller sea lions (SSL, Eumetopias jubatus; n=72) sampled in Alaska for C. burnetii antibodies, and vaginal swabs from NFS (n=40) for C. burnetii by qPCR. The antibody prevalence in NFS samples from 2009 and 2011 (69%) was significantly higher than in 1994 (49%). The antibody prevalence of SSL samples from 2007 to 2011 was 59%. All NFS vaginal swabs were negative for C. burnetii, despite an 80% antibody prevalence in the matched sera. The significant increase in antibody prevalence in NFS from 1994 to 2011 suggests that the pathogen may be increasingly common or that there is marked temporal variation within the vulnerable NFS population. The high antibody prevalence in SSL suggests that this pathogen may also be significant in the endangered SSL population. These results confirm that C. burnetii is more prevalent within these populations than previously known. More research is needed to determine how this bacterium may affect individual, population, and reproductive health of marine mammals.