Fourteen blood samples collected from dogs that were seropositive for Ehrlichia canis were examined for the presence of the citrate synthase gene using a highly specific and sensitive novel polymerase chain reaction assay. The assay detected E. canis DNA in 3 dogs. The complete nucleotide sequence of the citrate synthase gene was determined in 2 of the test-positive samples, and represents the first sequence of the gene to be derived from Italian isolates. The sequence data displayed high identity (99.2%) between the geographically separated Italian samples and the Oklahoma strain of E. canis. The high-sequence conservation revealed by molecular analysis confirmed the usefulness of the citrate synthase gene as a target for detection of E. canis.