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One hundred and twenty four patients, both male and females of different ages, visiting teaching hospital at the College of Dentistry /University of Mosul city / Iraq and from Private dentists clinics, who suffered from gingivitis disease in addition to 32 healthy people as controls, were subjected to examination by swabbing of gingival pockets for detection of Entamoeba gingivalis. Samples were diagnosed by conventional techniques of isolation, culturing and staining methods. The recovered positive isolates were subjected to molecular analysis. Amplification of DNA extracted from Entamoeba gingivalis of both diseased and healthy people using 18 rDNA revealed PCR products with 600pb size for both diseased and healthy people. Alignment of the DNA sequences of the isolates revealed sequences for two strains gp11 from the patients with gingivitis disease and gP45 strain from healthy people. This is first trial in Iraq in sequencing Entamoeba gingivalis isolates. Phylogenetic analysis of gp11 strain showed resemblance to that isolated in Japan, while gP45 strain to that isolated from Brazil.