Amoebiasis is the human infection with Entamoeba species, including E. histolytica, which is the causative agent of amoebic colitis, liver abscess, and rarely brain abscess; E. dispar, which is nonpathogenic; and E. moshkovskii, which causes diarrhea. The redefinition of E. histolytica, the re-description of E. dispar, and the recent results of isolation of E. moshkovskii from patients have dramatically changed the understanding of the prevalence of Entamoeba species in the population specifically in developing countries. These investigations have motivated researchers to develop a new diagnostic tools which are capable of differentiating the three species of morphologically indistinguishable Entamoeba encountered in clinical laboratories.Recently several molecular diagnostic methods have been developed for distinguishing E. histolytica / E. dispar / E. moshkovskii complex in developed countries, including new commercial multiplex PCR panels which offer high sensitivity, specificity, and ability to detect mixed infections. Molecular techniques will play an important role in diagnosis, epidemiological surveillance and outbreak studies. Also it considered as new diagnostic reference standard. The objective of the current review is to highlight the techniques that exist for the identification of Entamoeba species which are available in the clinical diagnostic laboratories. Moreover, numbers of newly published researches related to the molecular diagnosis of Entamoeba species are reviewed. Also it represents updating of the knowledge about molecular diagnostic techniques of amoebiasis within the period from 2013-up to date.