Despite distinct differences between walking and running, the two types of human locomotion are likely to be controlled by shared pattern-generating networks. However, the differences between their kinematics and kinetics imply that corresponding muscle activations may also be quite different. We examined the differences between walking and running by recording kinematics and electromyographic (EMG) activity in 32 ipsilateral limb and trunk muscles during human locomotion, and compared the effects of speed (3–12 km/h) and gait. We found that the timing of muscle activation was accounted for by five basic temporal activation components during running as we previously found for walking. Each component was loaded on similar sets of leg muscles in both gaits but generally on different sets of upper trunk and shoulder muscles. The major difference between walking and running was that one temporal component, occurring during stance, was shifted to an earlier phase in the step cycle during running. These muscle activation differences between gaits did not simply depend on locomotion speed as shown by recordings during each gait over the same range of speeds (5–9 km/h). The results are consistent with an organization of locomotion motor programs having two parts, one that organizes muscle activation during swing and another during stance and the transition to swing. The timing shift between walking and running reflects therefore the difference in the relative duration of the stance phase in the two gaits.