Background: Root canal treatment has been the main form of treatment for endodontic infections, and it comprises, chiefly, of physical instrumentation coupled with chemical irrigation. Objective: To compare the antibacterial effect of a diode laser and a Miswak (Salvadora persica) on Enterococcus faecalis in deep root canal dentin. Materials and Methods: A total of 500 extracted teeth with single rooted canal were collected randomly from different private dental clinics in Duhok city. The samples were collected using sterile red stopper plain plastic tubes. The samples were grouped in to two groups, 250 for the diode laser treatment and 250 for a miswak treatment, and inoculated into (Brain Heart Infusion agar and Blood agar) for the isolation and identification of Enterococcus faecalis. Results: Thirty (12%) isolates of E. faecalis were isolated from 250 single rooted canals, after treatment with diode laser 29 (96.7%) isolates were eliminated, whereas only 1 (3.3%) isolate was resistant to treatment with diode laser, while twenty eight (11.2%) isolates of E. faecalis were isolated from 250 single rooted canals, after injection with Miswak 27 (96.4%) isolates were eliminated, whereas only 1 (3.6%) isolate was resistant to Miswak activation. Conclusion: Both Diode laser and Miswak methods were very active in the elimination of E. faecalis isolated from infected single rooted canals.