The mandibular second molars show various morphological features in the roots and root canal, and a guttershaped root (GSR) caused by fusion of the mesial and distal roots is frequently encountered. In this study the number of the roots associated with mandibular second molars were observed using dental cone-beam computed tomography (CBCT). For those with a GSR, determination of root morphology and root canal classification were performed. CBCT image data from 173 Japanese mandibular second molars were obtained. Using sliced images, the number of the roots and root morphology were determined. In cases with a GSR, the ratio for the fused roots was determined and root canal morphology features were classified. A GSR was found in 61 (35.3%), with greater prevalence in females. In addition, the overall ratio of the fused part to root thickness in those with a GSR was 48.7%, with no significant difference related to sex. Furthermore, a C-shaped root canal morphology was commonly observed in both males and females with a GSR. In the present cohort examined in Japanese, most of the mandibular second molar were found to have two roots, with a GSR noted in 35.5%. While a GSR was more often observed in females, a C-shaped root canal was the most common root canal morphology in both sexs. It is considered that assessment using CBCT findings is helpful for precise determination of root canal morphology and presence of a GSR in mandibular second molars.