Background and objective: Intestinal and extraintestinal amebiasis is caused by the protozoan parasite Entamoeba (E.) histolytica, it is of considerable morbidity and mortality in developing countries. E.histoltica complex species includes E.histolytica, E. moshkovskii and E. dispar are morphologically indistinctable. The current study goal was to use molecular assays to detect the true prevalence of E. histolytica complex species among a cohort of Egyptians. Methods: A single stool specimen was collected from 133 patients, examined coproscopically before and after concentration. DNA was extracted from microscopically positive stool specimens for E. histolytica complex species were molecularly idenitified using multiplex PCR. Results: The coroscopic prevalence of intestinal parasites was 51.1% (68/133) of them 30 cases had E.histolytica complex (22.6%; 30/133). Among coproscopically positive samples, E. dispar was the most common parasite (63.3%; 19/30), followed by E. histolytica (23.4%; 7/30) and E. moshkovskii (13.3%; 4/30). There was statistical significance association between sociodemographic characteristics and Entamoeba species in asymptomatic individuals, while in the symptomatic individual, only age groups were stastically significant. Conclusion: E.dispar is the predominant Entamoeba species among studied individuals. There is a need for molecular diagnosis of Entamoeba to determine the true prevalence of E. histolytica and avoid overmedication.