The decline in the number of northern fur seal (NFS; Callorhinus ursinus) pups on St. Paul Island, Alaska, has led to multidisciplinary research, including investigation into issues of reproductive health and success. Given the recent identification of Coxiella burnetii in the placenta of two other marine mammal species, NFS placentas were collected from Reef rookery on St. Paul Island, Alaska, during the 2010 pupping season, examined histologically, and tested for C. burnetii using polymerase chain reaction (PCR). Of 146 placentas examined, gram-negative intratrophoblastic bacteria that were positive for C. burnetii on immunohistochemistry were observed in 5 (3%) placentas. Placental infection was usually devoid of associated inflammation or significant ancillary pathology. One hundred nine (75%) of the placentas were positive for C. burnetii on PCR. C. burnetii is globally distributed and persists for long periods in the environment, providing ample opportunity for exposure of many species. The significance of this finding for the declining fur seal population, potential human exposure and infection, and impact on other sympatric marine mammal or terrestrial species is unclear; further investigation into the epidemiology of Coxiella in the marine ecosystem is warranted.