Fishing affects the seabed habitat worldwide on the continental shelf. These impacts are patchily distributed according to the spatial and temporal variation in fishing effort that results from fishers' behaviour. As a consequence, the frequency and intensity of fishing disturbance varies among different habitat types. Different fishing methodologies vary in the degree to which they affect the seabed. Structurally complex habitats (e.g. seagrass meadows, biogenic reefs) and those that are relatively undisturbed by natural perturbations (e.g. deep-water mud substrata) are more adversely affected by fishing than unconsolidated sediment habitats that occur in shallow coastal waters. These habitats also have the longest recovery trajectories in terms of the recolonization of the habitat by the associated fauna. Comparative studies of areas of the seabed that have experienced different levels of fishing activity demonstrate that chronic fishing disturbance leads to the removal of high-biomass species that are composed mostly of emergent seabed organisms. Contrary to the belief of fishers that fishing enhances seabed production and generates food for target fish species, productivity is actually lowered as fishing intensity increases and high-biomass species are removed from the benthic habitat. These organisms also increase the topographic complexity of the seabed which has been shown to provide shelter for juvenile fishes, reducing their vulnerability to predation. Conversely, scavengers and small-bodied organisms, such as polychaete worms, dominate heavily fished areas. Major changes in habitat can lead to changes in the composition of the resident fish fauna. Fishing has indirect effects on habitat through the removal of predators that control bio-engineering organisms such as algal-grazing urchins. Fishing gear resuspend the upper layers of sedimentary seabed habitats and hence remobilize contaminants and fine particulate matter into the water column. The ecological significance of these fishing effects has not yet been determined but could have implications for eutrophication and biogeochemical cycling. Simulation results suggest that the effects of low levels of trawling disturbance will be similar to those of natural bioturbators. In contrast, high levels of trawling disturbance cause sediment systems to become unstable due to large carbon fluxes between oxic and anoxic carbon compartments. In low energy habitats, intensive trawling disturbance may destabilize benthic system chemical fluxes, which has the potential to propagate more widely through the marine ecosystem. Management regimes that aim to incorporate both fisheries and habitat conservation objectives can be achieved through the appropriate use of a number of approaches, including total and partial exclusion of towed bottom fishing gears, and seasonal and rotational closure techniques. However, the inappropriate use of closed areas may displace fishing activities into habitats that are more vulnerable to disturbance than those currently trawled by fishers. In many cases, the behaviour of fishers constrains the extent of the impact of their fishing activities. Management actions that force them to redistribute their effort may be more damaging in the longer term.