The role of brain asymmetries of dopaminergic neurons in motor symptoms of Parkinson’s disease is still undefined. Local field recordings from the subthalamic nucleus revealed some neurophysiological biomarkers of the disease: increased beta activity, increased low-frequency activity and high-frequency oscillations. Phase-amplitude coupling coordinates the timing of neuronal activity and allows determining the mechanism for communication within distinct regions of the brain. In this study, we discuss the use of phase-amplitude coupling to assess the differences between the two hemispheres in a cohort of 24 patients with Parkinson’s disease before and after levodopa administration. Subthalamic low- (12–20 Hz) and high-beta (20–30 Hz) oscillations were compared with low- (30–45 Hz), medium- (70–100 Hz) and high-frequency (260–360 Hz) bands. We found a significant beta-phase-amplitude coupling asymmetry between left and right and an opposite-side-dependent effect of the pharmacological treatment, which is associated with the reduction of motor symptoms. In particular, high coupling between high frequencies and high-beta oscillations was found during the OFF condition (P < 0.01) and a low coupling during the ON state (P < 0.0001) when the right subthalamus was assessed; exactly the opposite happened when the left subthalamus was considered in the analysis, showing a lower coupling between high frequencies and high-beta oscillations during the OFF condition (P < 0.01), followed by a higher one during the ON state (P < 0.01). Interestingly, these asymmetries are independent of the motor onset side, either left or right. These findings have important implications for neural signals that may be used to trigger adaptive deep brain stimulation in Parkinson’s and could provide more exhaustive insights into subthalamic dynamics.