A seroepidemiological survey was conducted in five bioclimatic areas of Tunisia to determine the prevalence of antibodies to Ehrlichia canis and Anaplasma phagocytophilum antigens, surrogate markers of the agents of canine monocytic ehrlichiosis (CME) and canine granulocytic ehrlichiosis, respectively. Among 286 collected sera, 54.2% and 25.2% were seropositive for E. canis and A. phagocytophilum, respectively, by the indirect immunofluorescence antibody (IFA) test. Clinical and hematological tests were done only for 58 sick dogs from Tunis area. A reverse line blot (RLB) hybridization was then used to identify isolated Ehrlichia and Anaplasma species infecting dogs (n = 228). Among them, only two dogs were infected by A. phagocytophilum; ten sample dogs were demonstrated infected by E. canis and ten infected by Ehrlichia sp., from which one dog showed a mixed infection with A. phagocytophilum and E. canis and one with A. phagocytophilum and Ehrlichia sp. RLB findings were confirmed by sequencing; BLAST search against GenBank revealed high similarity of the sequence of Ehrlichia sp. PCR/RLB amplicons with Anaplasma platys 16S rRNA partial sequence.