Polychlorinated biphenyls (PCB) and polybrominated diphenyl ethers (PBDE) levels were assessed in the liver and muscle of two data-deficient threatened dolphin species, the bottlenose dolphin (Tursiops truncatus, n = 4) and the Atlantic spotted dolphin (Stenella frontalis, n = 6), sampled off the Southeastern Brazilian coast. PCB concentrations were greater in liver compared to muscle, with males presenting higher concentrations than females. The three main detected PCB congeners were PCBs 138, 153 and 180. A predominance of hexachlorinated congeners was observed, followed by hepta- and penta-PCBs. For both species, Cl 3 and Cl 4 levels were higher in muscle compared to liver, while Cl 5 to Cl 8 and ∑PCBs were higher in liver. PBDE concentrations were significantly higher in Atlantic spotted dolphin muscle and liver compared to bottlenose dolphins. Similarly to PCBs, the highest PBDE concentrations were observed in males. The presence of PBDE congeners BDE-47, -100 and -99 in the muscle and liver of both species suggests the existence of a pollution source in Brazil by a penta-BDE mixture, as PBDEs have never been produced in Brazil. Interspecific PCB and PBDE profiles were very similar, which may be related to the similar characteristics of the analyzed species, mainly geographic distribution and life and feeding habits. This study furthers knowledge on environmental PCB and PBDE contamination, assisting in the establishment of dolphin population conservation strategies. In addition, this study calls into question the current threshold values established for PCBs and PBDEs, and demonstrates the lack of information and knowledge in this regard for cetaceans.