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Trawling for target species in many marine and coastal habitats directly damages those habitats and disrupts both ecosystem structure and function. Because these methods are generally non-selective, large numbers of non-target animals, along with undersized target species, may be swept up in nets; as well as benthic species being killed directly by trawl doors or drag chains. Additionally, abandoned fishing gear or "ghost fishing" poses a significant threat in some regions. As not all fishing methods are destructive, this is less of a widespread threat to habitats than overexploitation.
Blast fishing on coral reefs inherently destroys stony corals and kills fish and invertebrates in a large surrounding area. The resulting changes may lead to a decrease in biological diversity through a reduction in livable niches or through changes in ecosystem dynamics. A recent cost-benefit analysis calculated the economic cost to society for one blast fishery to be four times higher than the potential total net benefits offered to the region by tourism and coastal protection.
Fishing with cyanide or other poisons to stun and capture live aquarium and food fish for the restaurant retail business and the aquarium trade kills larvae of many coral-reef organisms and may add to the bleaching of corals. Several studies now show that habitat destruction through poison fishing is not as large as earlier anticipated. Estimates of the reef-degrading capacity of the cyanide fishery for food fish on Indonesia's coral reefs suggest a loss of live coral cover of .047 to .06 percentage points per year. This is significantly less than the threats noted for blast fishing (3.75% per year) or coral-bleaching events.