Mitochondria are crucial subcellular organelles for cell death and energy production. Mitochondrial dysfunction contributes to many human diseases. Gaining access to this organelle would create a powerful means for treating various diseases, including cancer. However, delivering bioactive materials to the mitochondria is hampered by the presence of the plasma membrane and mitochondrial membrane. To overcome this problem, we introduced a short cationic oligopeptide composed of histidines and arginines (H3R9) to the mitochondria-targeting sequence (MTS). Synthesized MTS-H3R9 was efficiently trans-localized to the mitochondria in HeLa cells according to confocal microscopy and flow cytometry studies. By combining these two distinct characteristics, cell-penetrating and mitochondria-targeting, MTS-H3R9 displayed much facilitated intracellular uptake and localization to the mitochondria. Such mitochondria-targeting peptides conjugated with functional peptides will enable effective translocalization of bioactive materials to the mitochondria.