Halogenated organic compounds (HOCs) in marine species collected from the Atlantic Ocean [3 shortfin mako (Isurus oxyrinchus) and 1 porbeagle (Lamna nasus)], and 12 sea turtles collected from the Pacific Ocean [3 loggerhead (Caretta caretta), 3 green (Chelonia mydas), 3 olive ridley (Lepidochelys olivacea), and 3 hawksbill (Eretmochelys imbricata)] were analyzed with a nontargeted analytical method using two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry. Sharks and sea turtles had distinct HOC profiles. Halogenated methoxyphenols (halo-MeOPs) were the most abundant compound class identified in sea turtle livers, while polychlorinated biphenyls (PCBs) were the most abundant in shark livers. In addition to legacy contaminants and halo-MeOPs, a total of 110 nontargeted/novel HOCs (NHOCs) were observed in the shark livers. Shortfin mako collected from the northern Gulf of Mexico contained the largest number (89) and most diverse structural classes of NHOCs. Among all NHOCs, a group of compounds with the elemental composition C₁₄H_12–nCl_n (n = 5–8) exhibited the highest concentrations, followed by chlorocarbazoles and tris(chlorophenyl) methanes (TCPMs). Using nontargeted workflows, a variety of known and unknown HOCs were observed, which demonstrate the need to develop more complete chemical profiles in the marine environment.