Due to the indistinguishable morphology between Entamoeba histolytica (pathogenic) and Entamoeba dispar (non pathogenic), PCR-based assays were conducted. Based on microscopy, suspected Entamoeba cells were detected in 30 out of 455 fecal samples obtained from individuals residing at Thai/Myanmar border region. The target genes for PCR amplification included genes encoding small subunit rRNA (SSU-rRNA), chitinase and serine rich Entamoeba protein. PCR primers derived from SSU-rRNA gene amplified both E. histolytica and E. dispar genes producing an amplicon of 1,080 bp, and detected 3 out of 30 samples. PCR primers derived from chitinase gene of E. histolytica generating amplicons of 500 and 1,260 bp, samples were positive in 12 out of 30 samples. Due the large difference of gene encoding serine rich protein between E. histolytica and E. dispar, two specific sets of primers were designed. SREH-primer set, specific for E. histolytica, generated amplicons of 550 and 700 bp and detected 22 out of 30 samples. SED-primer set, specific to E. dispar, produced an amplicon of 550 bp, and together with a nested primer pair generating an amplicon of 477 bp, detected 16 out of 30 samples. Thus, detection of single and mixed infections of the two Entamoeba species could be effectively achieved directly from DNA extracted from feces without the need to culture the parasites.