To handle the rich repertoire of behavioural goals, the CNS has to control the many degrees of freedom of the musculoskeletal system in a flexible manner. This problem can be drastically simplified if muscle synergies serve as the to-be-controlled building blocks of motor performance, instead of the individual degrees of freedom. Muscle synergies have been identified as coherent activation patterns of a group of muscles in space or time, but the neural mechanisms underlying their formation remain largely unknown. Here we evaluated the hypothesis that synergies are reflected in common input to different contributing muscles, and investigated modulations in motor unit (MU) synchronization of homologous muscles during a rhythmic balance task. If common input is related to muscle synergies, the resultant MU synchronization should not be static but task dependent and, in the present context, vary in time. Coherence between surface electromyographic signals of bilateral leg muscles revealed MU synchronization in two distinct frequency bands. MU synchronization was not constant but modulated within a movement cycle, and its time course resembled the activation patterns of the muscles. These results are congruent with a linkage between MU synchronization and muscle synergies, and suggest that MU synchronization provides an expedient method for studying synergy-related neural mechanisms.