Individuals with spinal cord injury (SCI) at lower thoracic levels might walk independently with the aid of mechanical orthoses and walker by using their unimpaired trunk and upper extremity muscles (TUEM). The required motor skills and the associated subtasks of the paraplegic locomotion, however, have not been well understood yet. The purpose of this study was to investigate the coordination of the TUEM activities throughout the paraplegic gait cycle using synergy analysis. For eight paraplegic individuals (30.6 ± 11.6 years; SCI level: T12), the kinematics data and the surface electromyography (EMG) signals of TUEM were recorded during 15 gait cycles. Non-negative matrix factorization method was used to extract muscle synergies from the EMG results, which were time normalized in association with four stages of each gait step. For each subject, the number, structures and activation profiles of the muscle synergies across different gait cycles were highly similar, resulting in three subject-specific templates of synergy structure and activation profile with mean intra-subject similarity scores of 0.94 ± 0.02 (p < 0.037) and 0.90 ± 0.06 (p < 0.001), respectively. Hierarchical clustering of the subject-specific templates revealed five representative templates for all subjects, among which, three that were in common for at least six subjects were considered as the characteristic synergies of paraplegic locomotion. The first and second characteristic synergies (inter-subject similarity scores >0.91, p < 0.037) composed mainly of the pectoralis major, latissimus dorsi, longissimus, iliocostalis quadratus lumborum, and the triceps, posterior deltoid and lower trapezius muscles, respectively, and were activated during the ipsilateral and the contralateral leg raising and swing stages. The third characteristic synergy, (inter-subject similarity scores >0.95, p < 0.02), contained mainly the abdominal and lumbopelvic muscles and was activated during the balance adjustment and walker propulsion stages of the gait cycle. These results provide more insight into the motor skills and the associated subtasks of the paraplegic locomotion. © 2018 Elsevier B.V.