This study aimed to determine the prevalence ofEntamoeba histolytica,Entamoeba disparandEntamoeba moshkovskii(collectively referred to asEntamoebacomplex), using microscopic and molecular methods in Kurdistan Province, northwest of Iran. The relationship between positiveEntamoebaspecies and clinical symptoms was also investigated. Eight positiveEntamoebacomplex, as well as fourEntamoebacomplex-like isolates, were detected by microscopic stool examination. DNA was extracted from all positive and from 55 randomly selected negative stool samples. PCR was performed using species-specific 18S rRNA primers for theEntamoebacomplex. All positive PCR samples were sequenced. In total, 14 (1.01%) out of 1383 isolates, i.e. 12 microscopy-positive andEntamoebacomplex-like isolates and two out of 55 microscopy-negative isolates, were identified via PCR and sequencing. Overall, 0.58% (8/1383) of the isolates wereE.dispar, 0.14% (2/1383)E.histolytica, 0.07% (1/1383)E.moshkovskiiand 0.22% (3/1383) were mixed ofE.histolyticaandE.dispar. Based on our findings, the prevalence ofE. disparis greater than that ofE. histoltyica. On the other hand, a case ofE. moshkovskiiwas reported for the first time in this region. It seems that some gastrointestinal symptoms may be attributed toEntamoebaspecies.