Anaplasma and Ehrlichia species are important bacterial pathogens of various animal species including dogs and humans. They constitute a major health problem worldwide, especially in the tropics and sub-tropics. In order to identify the prevalence of Anaplasma and Ehrlichia sp. from dogs in the selected area, a total of 100 randomly selected clinically healthy rescued dogs from animal shelters in Sarawak and Sabah, East Malaysia (50 dogs per State) were used for this study. Whole blood was collected from these dogs and screened for presence of Anaplasma and Ehrlichia spp. using polymerase chain reaction (PCR) and commercial ELISA test (SNAP 4Dx® Plus) for detection of antigen and antibody against the two pathogens respectively. 27% (A. platys) and 33% (E. canis) of the sampled population were positive using PCR; while the serological prevalence was 29% for Anaplasma sp. and 55% for Ehrlichia sp. The results of this investigation revealed that stray dogs are potential reservoir hosts of Anaplasma and Ehrlichia sp. infection with a high prevalence in the area. The high prevalence rates detected highlights the urgent need to address the growing population of possible vectors and reservoirs for transmission in the region and also to look into the public health aspect of the disease.