The most obvious ecological effect of longline fishing is that individuals of the targeted species are caught and processed. Commonly harvested fish in longline industries include tuna and billfishes, such as marlin and swordfish. These species are top-level predators that play key roles in the marine ecosystem, so their fisheries must be carefully regulated to prevent overfishing.
Commercial fishing ships use longline fishing to catch sharks for the lucrative shark-fin trade in Asia. Sharks fins are a popular delicacy in Asian cuisine, where they are used to make shark-fin soup. Because the fins are the most valuable part of the sharks and fishing ships have limited space, some longline fishermen actually catch more sharks than they can store, cut off their fins and throw the sharks back into the water where they bleed to death. Because sharks sit atop the oceanic food chain, lower populations can have major ecological impacts. Many countries ban this practice.
A signficant environmental impact of longline fishing is bycatch -- the incidental killing of non-targeted species. Longline fishing is designed to attract a particular target fish, but other creatures bite. These unintentional fish are called bycatch and include juvenile fish and other animals that can't be used for food. Some of these bycatch, such as sea turtles, albatrosses and other pelagic birds, dolphins, and whales are endangered. Although longline fishermen often try to reduce bycatch by using specialized hooks and attempt to return ensnared endangered animals to the water, often too much damage has already been done and the animal dies.
Another problem with longline fishing is entanglement. Sea birds, turtles and marine mammals that happen to be near the long fishing lines can get unintentionally ensnared. The hooks can tear or even tear off fins, wings and other body parts, killing the victims. This problem cannot be easily fixed with better hooks, since there's no way to stop animals from getting snared by the long lines.