BACKGROUND: Differentiation between Entamoeba histolytica and Entamoeba dispar is very important for both clinical therapy and epidemiological studies. Although these two species are morphologically identical, they have differences in genetic, chemical specifications and pathogenicity. This study was carried out to differentiate E. histolytica from E. dispar and also to find out frequency of the two species. METHODS: Fecal samples were collected three times from 655 patients with gastrointestinal complaints (47.3% male and 52.7% female), who were referred to the primary health care centers of Chelgerd, Chaharmahal and Bakhtiary province. Samples were examined microscopically with direct smear, formalin-ethyl-acetate concentration and trichrom staining methods to distinguish E. histolytica from E. dispar complex and differentiate them from non-pathogenic intestinal amoeba. Genomic DNA was extracted from microscopy positive isolates and polymerase chain reaction (PCR) was carried out to different the two morphologically identical Entamoeba isolates. RESULTS: Among the 655 recruited patients, eleven subjects with E. histolytica I E. dispar isolates (1.7%) were identified by microscopy methods. Ten of the positive isolates (90.9%) were identified as E. histolytica by PCR and one isolate (9.09 %) was positive for E. dispar. CONCLUSIONS: This study revealed that E. histolytica was more prevalent than E. dispar in the studied area. This result was different from the previously reported data in other parts of Iran