Ehrlichia chaffeensis is one of the causative agents of canine ehrlichiosis and human monocytic ehrlichiosis (HME). Canine ehrlichiosis caused by E. chaffeensis was diagnosed in two dogs in South Korea based on clinical findings, and the diagnosis was confirmed by polymerase chain reaction (PCR) and DNA sequencing. A 5-year-old intact male American Pit bull terrier allowed outdoors was found to be concurrently infected with Babesia gibsoni and E. chaffeensis. The major clinical findings were lethargy and reddish urine, and laboratory analysis revealed severe hematuria and thrombocytopenia. In addition, a 3-year-old neutered male Shih-tzu was also found to be infected with E. chaffeensis. Although this dog was an indoor companion animal, he was frequently allowed outside for exercise. The clinical signs observed in this dog included generalized purpura with petechiae and ecchymoses due to thrombocytopenia. A 390-bp partial portion of E. chaffeensis 16S rRNA gene was amplified in both cases, and nucleotide sequence analysis revealed 99% homology of this fragment with other E. chaffeensis isolates. These findings demonstrate the presence of E. chaffeensis infection in dogs in South Korea, and this is the first report to confirm clinical cases of E. chaffeensis infection in dogs.