Cysts of Entamoeba histolytica are still found from humans in Korea, but not all of the cysts are known as pathogenic. The non-pathogenic strain is regarded as a different species, E. dispar. In this study, Korean isolates of conventional E. histolytica were subjected for the differentiation by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Human stools were screened by routine microscopic examination, and cyst or trophozoite positive stools were inoculated into Robinson media. The cultivated trophozoite positive stools were inoculated into Robinson media. The cultivated trophozoites were prepared for DNA extraction, and the DNAs were used for PCR with common primers of P1 gene. The PCR products were digested with 3 restriction enzymes and RFLP was observed. Also anti-sense primers containing the cleavage site of each restriction enzyme were designed for differentiation only by PCR. The PCR products of Korean isolates S9, S12, YS-6, and YS-27 were spliced by Taq I and Xmn I but not by Acc I, and the isolates S1, S3, S11, S15, S16, S17, S20, YS-17, and YS-44 were spliced by Acc I but not by Taq I and Xmn I. These RFLP pattern correlated well with PCR products by the species specific primers. The findings confirm that the Korean isolates S9, S12, YS-6, and YS-27 are E. histolytica and others are E. dispar. In Korea, most of the asymptomatic cyst carriers are infected by E. dispar, not by E. histolytica.