The subthalamic nucleus (STN) and zona incerta (ZI) are two subthalamic brain structures involved in several neuron circuitries controlling important functions including motor, limbic and cognitive behaviors. Cre-driven reporter analysis of coronal brain sections of the transgenic mouse lines PVCre/GFP-Sun1 and Pitx2Cre/GFP-Sun1 were used to distinguish internal cellular organization of the STN and ZI, facilitating the establishment of potential borders. This study detected GFP positive neurons in the medial-ventral ZI and in the dorsolateral STN in the PVCre/GFP-Sun1 transgenic mouse line. Across the entire STN, GFP expression in the Pitx2Cre/GFP-Sun1 transgenic mouse line could be detected. In addition, GFP positive neurons in the Pitx2Cre/GFP-Sun1 transgenic mouse line were sparsely detected in the para-subthalamic nuclei (PSTN) and totally absent within the ZI area. Studies investigating the internal cellular organization of the STN and ZI by distinguishing domains and their neurotransmitter phenotype are of clinical relevance in Deep Brain Stimulation (DBS) treatment for brain disorders.