Anatomical Variation in the number of roots or root canals poses challenges in the endodontic treatment. Mandibular first molars presents various anatomical variation which have been studied and reported namely radix entomolaris, paramolaris, C shaped canals, mid mesial/ distal canal, taurodontism etc. Thorough knowledge of anatomy of apical canal merging in Type II canal configuration and Radix entomolaris is of importance with respect to the shaping of the canal and conserving the tooth structure. Also, there is a high risk of Instrument separation with NiTi rotary instrument when there is apical confluences and acute angle of root curvatures. Radix entomolaris in mandibular molars and Type II canal configuration have been widely reported in the literature involving other teeth but management of Type II mesial canal configuration has not been reported in mandibular molars. This case report describes the successful nonsurgical endodontic management of radix entomolaris along with Type II canal morphology with separated instrument in the mesial root of mandibular first molar using CBCT.