The prevalence of amoebiasis is often overestimated owing to its epidemiological overlap with the non-pathogenic Entamoeba dispar. To provide evidence for this conjecture, a cross-sectional study was conducted from November 2013 to January 2015. A range of 180–200 µg of semi-solid and formed stools and 200 µL of diarrhoeic stool samples were used for DNA extraction from microscopically E. histolytica/dispar positive samples using the QIAamp® DNA Stool Mini Kit according to manufacturers’ instructions. Nested PCR targeting 18S ribosomal RNA gene was used. In 422 microscopically positive E. histolytica/dispar stools, molecular prevalence revealed that E. histolytica infestation was present in only 1.7% (95% confidence interval [CI], 0.47–2.93) and E. dispar was found in 42.2% (95% CI, 37.49–46.91), while 56.2% (95% CI, 51.47–60.93) had neither E. histolytica nor E. dispar (P < 0.001). We conclude that infestation with E. histolytica is rarer in our study areas than was previously believed. Hence, accurate differentiation of E. histolytica and E. dispar is crucial.