The use of substances that modulate mitochondrial dynamics in cells of nervous tissue represents a new direction in targeted therapy for neurodegeneration. The aim of this study was to evaluate the effect of mitochondrial division inhibitor-1 (Mdivi-1) on neurons and microgliocytes of the substantia nigra under conditions of partial damage to the dopaminergic system. This study was conducted using the 6-hydroxydopamine model of parkinsonism in rats; a separate experimental group of animals received Mdivi-1 intraperitoneally at a dose of 20 mg/kg for 5 days. The intensity of immunofluorescence staining for Tomm20, MTCO1, pDrp1, and Mfn2 was evaluated in neurons of the substantia nigra, and microglial activation was morphologically assessed. It was found that unilateral administration of 6-OHDA led to pro-inflammatory changes in microglia and changes in mitochondrial markers of neurons on the side of the substantia nigra contralateral to the toxin injection. Mdivi-1 did not affect the damage and mitochondrial proteins of neurons in pars compacta of the substantia nigra; however, it changed mitochondrial markers in nervous cells of the pars reticulata. The use of Mdivi-1 to address abnormal processes in neurodegeneration requires additional studies that include a differential assessment of its effects on various cell types.