There has been extensive debate as to whether muscle synergies in motor tasks reflect underlying neural organization or simply correlations in muscle activity that are imposed by the task. One possible means of distinguishing these two alternatives is through the analysis of variability in the electromyogram (EMG). Here, we simulated EMG in eight lower-limb muscles and introduced hypothetical neural coupling between specific muscle groups. Neural coupling was simulated by introducing correlations in the neural activation commands to different muscles (positive, negative, or zero coupling). When the entire EMG signal was used for analysis, the extracted synergies reflected only simultaneous muscle activity, regardless of the neural coupling between the muscles. On the other hand, examining the variability in the EMG after subtracting the ensemble average was successful in identifying the simulated neural coupling. The extracted synergies from these two methods were also different when we analyzed data from participants during treadmill walking. The results emphasize the importance of examining EMG variability to understand the neural basis of muscle synergies.