Oral cavity cancers (OCC) represent approximately 25 to 30% of cancers of the upper aero digestive tract (UAT) i.e. head and neck carcinomas. OCC is the 4th most common cancer in men and the14th most frequent among women worldwide. Here, we aimed to determine the variability and genetic diversity of two mitochondrial markers, namely MT-CYB and D-Loop, in cancerous tissues and control subjects with OCC in Senegal. A total of 45 patients with OCC were enrolled as subjects. Blood sample and biopsy of the tumor were obtained from each patient and total DNA was extracted from the samples. Our study highlighted the feminization and rejuvenation of the pathology with 62% women compared with 38% men. The mean age of our patients was 53 ± 16.64 years. The most frequent location of the tumor was the gum with 42% of cases. Nine amino acids showed a significant mean difference between healthy and cancerous tissues. For the molecular characterization of OCC, D-Loop and MT-CYB genes were amplified and sequenced. Notably, cancerous tissues were more polymorphic than healthy tissues for both D-Loop and MT-CYB. Furthermore, MT-CYB was more polymorphic than D-Loop in patients with OCC in Senegal. Our study also confirmed the major role of tobacco in the occurrence of OCC. Together, our results are in agreement with previous studies, and further implicate D-Loop and MT-CYB polymorphism in OCC tumor progression and development.