Patagonia and Antarctica are biodiverse regions in the Southern Hemisphere, but little is known about the levels of trace elements in marine organisms from these remote coastal ecosystems. In this study, selenium (Se), copper (Cu), zinc (Zn), and stable isotopes of nitrogen (δ15N; relative trophic level) were measured in 36 marine species collected from two locations of the Chilean Patagonia and two locations of the Antarctic Peninsula area to determine whether biomagnification of these trace elements occurs in the food webs. Results indicated that Cu, Se, and Zn levels were slightly lower than those in similar species from elsewhere, and the highest metal levels were found in marine macroinvertebrates compared with fishes. There was evidence of Cu, Se, and Zn biomagnification but only within the lower-trophic-level organisms. When assessing whole food webs, levels of these elements typically decreased from macroinvertebrates to fishes or birds, suggesting lower risks of metal toxicity to higher-level consumers.