Amoebiasis caused by Entamoeba histolytica, is a major public health problem in developing countries. Morphologically similar E. dispar is non pathogenic. Because of the redefinition of E. histolytica and E. dispar, and the limited number of antiamoebic drugs available, a new approach to treat such individuals is necessary. The cost of treating asymptomatic individuals is highly exorbitant and not justifiable. The indiscriminate use of antiamoebic drugs can result in increased minimum inhibitory concentration (MIC) values against Entamoeba species, and treatment failure may emerge as an important public health problem. Development of new antiamoebic drugs is still in infancy and vaccine development appears to be distant dream. In future, the development of drug resistance may seriously affect the control of disease. This review discusses the factors involved in drug resistance mechanisms developed by the parasite.