Cetaceans accumulate persistent and toxic substances such as polybrominated diphenyl ethers in their tissue. PBDEs are ubiquitous in marine environments, and their exposure to mammals is linked to numerous health effects such as endocrine disruption, neurotoxicity, carcinogenicity, and fetal toxicity. However, the toxicological effects and mechanism of toxicity in cetaceans remains poorly understood. The effects of BDE-47 (0.1–0.5 μg mL−1), BDE-100 (0.1–0.5 μg mL−1), and BDE-209 (0.25–1.0 μg mL−1) exposure on cell viability, oxidative stress, mitochondrial structure, and apoptosis were evaluated using a recently established pantropical spotted dolphin (Stenella attenuata) skin fibroblast cell line (PSD-LWHT) as an in vitro model. However, the production of reactive oxygen species (ROS) increased following exposure to 1.0 μg mL−1 PBDE while superoxide anion, hydroxyl radicals, and inducible nitric oxide increased in a dose-dependent manner. At 0.5–1.0 μg mL−1, PBDEs significantly reduced the mitochondrial membrane potential. In addition, exposure to BDE-47 and -209 significantly affected mitochondrial structure as well as cell signaling and transduction compared to BDE-100. Although PBDE exposure did not affect cell viability, a significant increase in cell apoptosis markers (Bcl2 and caspase-9) was observed. This study demonstrated that BDE-47, -100, and −209 congeners might cause cytotoxic and genotoxic effects as they play a crucial role in the dysregulation of oxidative stress and alteration of mitochondrial and cell membrane structure and activity in the fibroblast cells. Hence, these results suggest that PBDEs might have adverse health effects on cetaceans inhabiting contaminated marine environments.