Bottom trawling and use of other mobile fishing gear have effects on the seabed that resemble forest clearcutting, a terrestrial disturbance recognized as a major threat to biological diversity and economic sustainability. Structures in marine benthic communities are generally much smaller than those in forests, but structural complexity is no less important to their biodiversity. Use of mobile fishing gear crushes, buries, and exposes marine animals and structures on and in the substratum, sharply reducing structural diversity. Its severity is roughly comparable to other natural and anthropogenic marine disturbances. It also alters biogeochemical cycles, perhaps even globally. Recovery after disturbance is often slow because recruitment is patchy and growth to maturity takes years, decades, or more for some structure-forming species. Trawling and dredging are especially problematic where the return interval-the time from one dredging or trawling event to the next-is shorter than the time it takes for the ecosystem to recover; extensive areas can be trawled 100-700% per year or more. The effects of mobile fishing gear on biodiversity are most severe where natural disturbance is least prevalent, particularly on the outer continental shelf and slope, where storm-wave damage is negligible and biological processes, including growth, tend to be slow. Recent advances in fishing technology (e.g., rockhopper gear, global positioning systems, fish finders) have all but eliminated what were de facto refuges from trawling. The frequency of trawling (in percentage of the continental shelf trawled per year) is orders of magnitude higher than other severe seabed disturbances, annually covering an area equivalent to perhaps half of the world's continental shelf, or 150 times the land are that is clearcut yearly. Mobile fishing gear can have large and long-lasting effects on benthic communities, including young stages of commercially important fishes, although some species benefit when structural complexity is reduced. These findings are crucial for implementation of "Essential Fish Habitat" provisions of the U.S. Magnuson-Stevens Fishery Conservation and Management Act which aim to protect nursery and feeding habitat for commercial fishes. Using a precautionary approach to management, modifying fishing methods, and creating refuges free of mobile fishing gear are ways to reduce effects on biological diversity and commercial fish habitat.