To elucidate the underlying physiological mechanisms of muscle synergies, we investigated long-range functional connectivity by cortico-muscular (CMC), intermuscular (IMC) and cortico-synergy (CSC) coherence. Fourteen healthy participants executed an isometric upper limb task in synergy-tuned directions. Cortical activity was recorded using 32-channel electroencephalography (EEG) and muscle activity using 16-channel electromyography (EMG). Using non-negative matrix factorisation (NMF), we calculated muscle synergies from two different tasks. A preliminary multidirectional task was used to identify synergy-preferred directions (PDs). A subsequent coherence task, consisting of generating forces isometrically in the synergy PDs, was used to assess the functional connectivity properties of synergies. Overall, we were able to identify four different synergies from the multidirectional task. A significant alpha band IMC was consistently present in all extracted synergies. Moreover, IMC alpha band was higher between muscles with higher weights within a synergy. Interestingly, CSC alpha band was also significantly higher across muscles with higher weights within a synergy. In contrast, no significant CMC was found between the motor cortex area and synergy muscles. The presence of a shared input onto synergistic muscles within a synergy supports the idea of neurally derived muscle synergies that build human movement. Our findings suggest cortical modulation of some of the synergies and the consequential existence of shared input between muscles within cortically modulated synergies.