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Enterococcus faecalis as natural flora are found in the intestines of humans and animals, as well as in the female reproductive system, in the oral cavity and sometimes in the respiratory tract, as well as in soil and water. One hundred samples of patients with root canal infections were collected in primary and secondary injuries to the root of the tooth canal, referred to the Tikrit Dental Center and the Faculty of Dentistry at Tikrit University, and for 9/10/2021 to 3/3/2022 and for ages ranging from 20 to 60 years. Culture and Vitec test were performed as well as PCR assay. The results showed that the proportion of isolations was higher in secondary injuries, particularly in age ranging from 25 to 50 years, although the proportion of samples taken from people with tooth roots inflammation after the failure of treatment was lower than those taken from people with primary root canal inflammation, due to difficulty in obtaining such samples. The results of genetically based molecular diagnosis of bacteria showed that (32) isolation from diagnosed samples was due to the type of fecal intestinal cocci. The results also show a high percentage of fecal intestinal cocci (32%) in the injuries of the roots of the teeth, and the results of the molecular diagnosis showed a clear difference from those obtained using chemical methods in diagnosis.