Methods such as Cyanide Poisoning, Dynamite Fishing, Bottom Trawling and Long-line Fishing are still widely practiced for catching large amounts of fishes. These practices affects the marine life adversely. Blasting kills coral reefs and animals that live around them. It destroys 200 square feet of coral reef at a time while cyanide stuns fishes for them to be easily caught as they are unable to escape. It is estimated that, over the past 25 years, the damage caused by dynamite fishing to reef ecosystems has resulted in the loss of US$3.8 billion dollars of income to Indonesia. Therefore, though these are short term gains, it results in large and severe compensations in the long run.

Bycatch also means the accidental capture of non-targeted species such as dolphin, marine turtles and seabirds while fishing. Every year, through the use of gillnets, on longlines and in trawls, millions of pound of non-target fish species and other marine life are caught and often discarded back into sea either dead or dying. This happens because modern fishing gears used, efficient at catching the desired fish species, are often undetectable by sight and extremely strong to catch anything in its path.

Overfishing is a result when more fishes are caught than the population can replace through natural reproduction. This is a serious problem in the Coral Triangle for many different species due to the rapidly increasing demand of fish. Billions of people rely on fish for protein and fishing in the principal livelihood for millions of people around the world.  Though gathering as many fish as possible seems to be a profitable practice, it leads to the imbalance of life in the oceans and affect social and economic well-being of the coastal communities who depend on fish for survival. The over exploitation of the waters has threatened the survival of many species within the seas. Many fishermen and companies are aware of the need to manage and protect the fish populations and the natural environment, however, illegal fishing and other regulatory inefficiencies still exist and need to be solved efficiently to properly manage this problem.