Parkinson’s disease (PD) is a progressive neurodegenerative disorder. Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a common target for treating PD's motor symptoms. However, we have little understanding of STN pathology in PD. We aimed to examine the cellular and functional pathology of the STN in PD using both rodent and post-mortem human brain tissue. First, we show bidirectional motor control by STN using optogenetic modulation, where inhibition of the STN increases movement and STN activation decreases movement. We also examined the effect of bidirectional optogenetic manipulation of STN neuronal activity under dopamine-depleted conditions using the bilateral rodent 6-hydroxydopamine (6-OHDA) model of PD. Optogenetic inhibition of the STN in the absence of dopamine had no impact on motor control, yet STN excitation led to pronounced abnormal involuntary movement. Administration of levodopa rescued the abnormal involuntary movements induced by STN excitation. Using post-mortem brain tissues from PD and age-matched controls were stained with markers for neurodegeneration. As expected, significant neuronal cell loss, alpha-synuclein pathology, and variable astrogliosis were observed in the SN in PD. No neuronal cell loss or astrogliosis was observed in the STN, although alpha-synuclein deposition was present in the STN in all PD cases. This study reports selective pathology in the STN with alpha-synuclein deposits in the absence of significant neuronal cell loss or inflammation in PD. Overall, these studies reveal insight into the STN pathology in PD and the therapeutic mechanism of targeting the STN for the treatment for PD.