It remains unknown how the human brain generates coordinated patterns of muscle activity. Here we examine competing hypotheses - one in which the motor cortex “activates” coordination patterns that are subcortically encoded, and one in which the motor cortex “structures” coordination patterns by co-activating distinct neural populations that output to separate muscles with different functions. To disambiguate these hypotheses, we exploit properties of coordination between pelvic floor and gluteal muscles in humans. Using electromyography (EMG), we first show that the brain can voluntarily access two main types of coordination patterns with these muscles:​ one activates pelvic floor muscles independently of gluteal muscles (isolated-pelvic), and a second activates the pelvic floor prior to but in proportion with gluteal muscles (gluteal-pelvic). Using functional magnetic resonance imaging (fMRI), we show that isolated-pelvic and gluteal-pelvic coordination patterns involve very similar motor cortical representations, suggesting the presence of intermingled neural populations with distinct muscle function that can be independently activated. Using transcranial magnetic stimulation (TMS), we show that pelvic floor potentials can be evoked during rest but that gluteal potentials can only be evoked after voluntary pre-activation of gluteals, suggesting that the distinct motor cortical populations are distinguished by activation threshold. TMS did not reveal any delay in evoked gluteal potentials relative to evoked pelvic floor potentials as would be predicted by the activation hypothesis. We propose that common input to distinct neural populations with different activation thresholds provides a mechanism by which the nervous system may structure spatiotemporal muscle coordination at a motor cortical level.