Previous kinematic analyses in Sceloporus clarkii have shown that increased speed during trotting is attained by retracting the femur relatively faster (decreasing retraction time relative to stride duration) while all other aspects of axial and limb movements occur simply faster (scaling with stride duration). Thus, most of the limb muscles must be modulated to move the joints absolutely faster, while muscles effecting femoral retraction must be modulated differently to retract the femur relatively faster to increase speed. This prediction was examined by analyzing motor patterns in several key leg muscles in the spiny lizard running over a threefold increase in speed during a trot. The prediction is borne out in the limb muscles where the limb adductor (flexor tibialis), knee extender (femorotibialis), and plantar flexor of the ankle (gastrocnemius) have similar patterns of motor modulation that are different from that of the femoral retractor (caudofemoralis). To modulate a muscle to move simply faster (scaled with speed) the offset of the motor pattern is moved relatively earlier to decrease burst duration, while the intensity of electromyographical activation is ramped up. Increasing the relative speed of action is done by activating the muscle earlier, increasing the duration of the burst, and increasing the relative level of activation. Comparisons to other studies illustrate that the confounding effects that stance and swing duration have on stride duration with speed have important consequences for functional interpretations and that scaling locomotory data to stance duration is a more appropriate and useful convention because it relates information directly to the duty cycle when the propulsive effects of motor modulation are transmitted to the substrate. The iliocostalis in Sceloporus clarkii has a pattern of activity indicating that it functions to rotate the pelvis to aid the contralateral duty cycle. This is strikingly different from the function of the iliocostalis in the monitor lizard. Differences in axial function and differences among lizards in postures of the foot and crus during locomotion indicate that there are different ways that lizards run and that the functional and anatomical diversity of modes of locomotion in lizards is greater than is recognized at present.