Correlation of spontaneous fluctuations at rest between anatomically distinct brain areas are proposed to reflect the profile of individual a priori cognitive biases, coded as synaptic efficacies in cortical networks. Here, we investigate functional connectivity at rest (rs-FC) in musicians and nonmusicians to test for differences in auditory, motor, and audiomotor connectivity. As expected, musicians had stronger rs-FC between the right auditory cortex (AC) and the right ventral premotor cortex than nonmusicians, and this stronger rs-FC was greater in musicians with more years of practice. We also found reduced rs-FC between the motor areas that control both hands in musicians compared with nonmusicians, which was more evident in the musicians whose instrument required bimanual coordination and as a function of hours of practice. Finally, we replicated previous morphometric data to show an increased volume in the right AC in musicians, which was greater in those with earlier musical training, and that this anatomic feature was in turn related to greater rs-FC between auditory and motor systems. These results show that functional coupling within the motor system and between motor and auditory areas is modulated as a function of musical training, suggesting a link between anatomic and functional brain features.