The objective of the present article was an epidemiological and molecular study of Ehrlichia canis in dogs of Ilhéus and Itabuna in Bahia, as well as an evaluation of associated risk factors. Blood samples were collected from 153 dogs and DNA was extracted and analyzed by the nested-polymerase chain reaction, using one pair of primers to detect Ehrlichia bacteria and another pair to detect the presence of E. canis. Of the 153 animals, 12 (7.8%) were polymerase chain reaction-positive for E. canis, indicating the presence of the parasite in dogs of the Ilhéus-Itabuna microregion. The associated risk factors were exposure to tick-infested habitats and the fact that the dogs lived in the countryside.