All 18 species of penguin are legally protected from hunting and egg collecting. The Antarctic Treaty of 1959 makes it illegal to harm, or in any way interfere with, a penguin or its eggs. Every penguin specimen collected with a permit must be approved by and reported to the Scientific Committee for Antarctic Research (SCAR). Penguins are vulnerable to habitat destruction, overfishing of primary food sources, ecological disasters such as oil spills, pollution such as trash in the ocean, and human encroachment into nesting areas.

Current threats to Magellanic penguins include overfishing of anchovies (a primary food source), habitat destruction and pollution. Due to their long migrations to reach their breeding grounds, Magellanic penguins are known to be soaked by oil as they swim through heavily travelled ocean shipping lanes.