The specificity and sensitivity demonstrated by the SYBR Green real-time PCR protocols indicate an interesting approach to the identification and differentiation of these Entamoeba species. The application of those protocols in different regions can be a helpful tool to provide more reliable parasitological diagnosis and more detailed epidemiological data on the prevalence of Entamoeba species around the world. The combination of both real-time PCR protocols may allow the development of a simple and useful Entamoeba identification system to improve the laboratory diagnosis of amoebiasis in developing countries.