The regulation of mitochondrial biogenesis, melanogenesis, and connective tissue proteins is critical for homeostasis and aging skin cells. We examined the biological effects of polydeoxyribonucleotide (PDRN) on mitochondrial biogenesis, melanogenesis, and connective tissue proteins in vitro. In a radical scavenging assay, PDRN showed antioxidant activities in a dose-dependent manner, and those activities can suppress cellular oxidative stress in skin cells. PDRN directly inhibited mushroom tyrosinase activity and cellular tyrosinase activity, thus significantly reducing the cellular melanin content in B16-F10 melanocytes. The mRNA and protein expressions of the microphthalmia-associated transcription factor (MITF), which is a key melanogenic gene transcription factor, were significantly downregulated by PDRN. Accordingly, tyrosinase-related protein 1, dopachrome tautomerase, and tyrosinase, which gene expressions were regulated by MITF, were significantly downregulated by PDRN. Mitotracker-probed mitochondria image analysis suggested that PDRN enhanced mitochondrial density in both murine melanoma cells and in human skin fibroblast cells. In addition, PDRN strongly suppressed in vitro elastase enzyme activity in a dose-dependent manner and inhibited matrix metalloproteinase-1 gene expression in human skin fibroblast cells. Collectively, these findings indicate that PDRN has multiple beneficial biological activities in skin cells: hypopigmentation, induction of mitochondrial biogenesis, and the inhibition of collective tissue proteins.