One is drift netting. These nets are indiscriminate and also catch, injure and kill fishes that are not intended to be caught. This, therefore, greatly affects the marine ecosystem.
Second is over-fishing. This reduces the fish population to a point where they are unable to regenerate and hence predisposes/ condemning them to extinction
Third is the destruction of marine ecosystem, deliberately, to clear an obstacle or pave the way for fishing lines. This damages the habits hence affecting the ecosystem from primary producers and up the food chain.