It is well established that the motor cortex makes an important contribution to the control of visually-guided gait modifications, such as those required to step over an obstacle. However, it is less clear how the descending cortical signal interacts with the interneuronal networks in the spinal cord to ensure that precise changes in limb trajectory are appropriately incorporated into the base locomotor rhythm. Here we suggest that subpopulations of motor cortical neurones, active sequentially during the step cycle, may regulate the activity of small groups of synergistic muscles, likewise active sequentially throughout the step cycle. These synergies, identified by a novel associative cluster analysis, are defined by periods of muscle activity that are co-extensive with respect to the onset and offset of the EMG activity. Moreover, the synergies are sparse and are frequently comprised of muscles acting around more than one joint. During gait modifications, we suggest that subpopulations of motor cortical neurones may modify the magnitude and phase of the EMG activity of all muscles contained within a given synergy. Different limb trajectories would be produced by differentially modifying the activity in each synergy thus providing a flexible substrate for the control of intralimb coordination during locomotion.