Mobile fishing gear affects biodiversity and habitat in New England offshore waters through selective fishing activity, seabed disturbance, and discarding and encounter mortality. Selective fishing activity results in geographically localized impacts on habitat and more widespread impacts on biodiversity through the selective removal of specific species with a higher economic value. Seabed disturbance by fishing activity results in physical impacts related to resuspension of fine sediments and scarring of the seabed, chemical effect due to resuspension of nutrients, and biological impacts related to alteration of the benthic community structure. Discards and other benthic fauna that encounter mobile gear and are impacted by the interaction, temporarily alter the ecosystem dynamic. In general, the habitat impacts are restricted to areas of heavy fishing activity, and in shallower water are ameliorated by natural processes that regularly disturb the seabed. Effects on biodiversity are more widespread due to the transient nature of many impacted species. Mobile fishing gear produces approximately 75% of the landings from New England offshore waters. Habitat impact and a loss of biodiversity may be considered a cost of seafood production. Preservation of habitat and biodiversity in marine sanctuaries and reserves is recommended to balance the effects of fishing. This is analogous to society's management strategy in the terrestrial environment.