Numerous studies have explored root anatomy and root canal morphology variations across ethnic groups, but few have focused on the Jordanian population. This study, aimed to assess the prevalence of root anatomy and canal morphology in permanent teeth of a Jordanian subpopulation using cone-beam computed tomography (CBCT). This part of a four-part series focused on mandibular first and second molar teeth. Subsequent parts will address the root anatomy and canal morphology of (1) mandibular anterior teeth, (2) maxillary molars, and (3) maxillary and mandibular premolars. CBCT scans of 332 mandibular molars from patients treated at The University of Jordan Hospital between June and December 2022 were analysed. Canal configurations were categorized according to Vertucci’s classification. The majority of mandibular first and second molars had two roots (96.2% and 85%, respectively), with variations such as a third root or a single C-shaped root. Most mesial roots had two canals (100% of first molars, 98.6% of second molars), and distal roots predominantly had one canal (77.9% of first molars, 97.4% of second molars). The most common mesial canal configuration was type II (68% in first molars, 83.7% in second molars), while type I was most common in distal roots (77.8% in first molars, 97.4% in second molars). No significant gender-related differences were found. The study also revealed asymmetry in root morphology between the right and left sides. The root and canal morphology of Jordanian mandibular molars closely resembled the average features observed in Arab and Caucasian populations.