Functional electrical stimulation (FES) facilitates ambulatory function after paralysis of persons with spinal cord injury (SCI) by exciting the peripheral motor nerves to activate the muscles of the lower limbs. This study identified a process for selecting command sources for triggering FES with the surface electromyogram (EMG) from muscles partially paralyzed by incomplete SCI, given its high degree of intersubject variability. We found Discriminability Index (DI) to be a good metric to evaluate the potential of controlling FES-assisted ambulation in four nondisabled volunteers and two participants with incomplete paralysis. The left erector spinae (ES) (mean DI = 0.87) for triggering the left step and the right ES (mean DI = 0.83) for triggering the right step were the best command sources for participant 1. The left ES (mean DI = 0.93) for triggering the left step and the right medial gastrocnemius (mean DI = 0.88) for triggering the right step were the best command sources for participant 2. Our results showed that command sources can be selected objectively from surface EMG before a fully implantable EMG-triggered FES system for walking is implemented.