Abundance of many Atlantic cod (Gadus morhua) and groundfish stocks in the Northwest Atlantic declined to low levels in the early 1990s, resulting in cessation of directed fishing for these stocks, thus ending one of the largest and longest running commercial groundfish fisheries in the world. The stocks of the northern (nGSL) and southern Gulf of St. Lawrence (sGSL) were closed to directed cod fishing from 1994 to 1996 for the nGSL and from 1993 to 1997 for the sGSL, followed by the opening of a small directed fishery in the two systems. In the northern Gulf of St. Lawrence, the ecosystem biomass structure shifted dramatically from one dominated by demersal fish predators (Atlantic cod Gadus morhua, redfish Sebastes spp.) and small-bodied forage species (capelin Mallotus villosus, mackerel Scomber scombrus, herring Clupea harengus, northern shrimp Pandalus borealis) to one now dominated by only small-bodied forage species. The decline of large predatory fishes has left only marine mammals as top predators during the mid-1990s, and marine mammals and Greenland halibut Reinhardtius hippoglossoides during the early 2000s. Large changes also occurred in the biomass structure and ecosystem functioning of the adjacent southern Gulf of St Lawrence (sGSL) but they were not as dramatic. Although predatory fishes decreased between the mid-1980s and mid-1990s, and prey consumption by seal species increased considerably, large cod remained among the most important single predators on fish in the sGSL. The changes in top-predator abundance driven by human exploitation of selected species resulted in a major perturbation of the structure and functioning of both Gulf ecosystems and represent a case of fishery-induced regime shift. Overfishing influenced community biomass structure directly through preferential removal of larger-bodied fishes and indirectly through predation release. Species interactions are central to ecosystem considerations. In marine ecosystems, predation can be the major ecological process affecting fish populations and piscivory is often the largest source of fish removal, usually larger than fishing mortality. In both northern and southern Gulf ecosystems, predation mortality exceeded fishing mortality for most groups in recent years because fishing mortality was intentionally reduced by fisheries closures. Seals have benefited from reduced hunting (harvesting and culling/bounties) since the 1970s. Consumption of fish by marine mammals exceeded consumption by predatory fishes in the two ecosystems in the recent time periods. Since the collapse of groundfish stocks, commercial fisheries and seals have become important predators on predatory fishes possibly slowing their recovery. In recent years, consumption by seals shifted towards species at lower trophic level (forage fishes and invertebrates), which were also the main target of fisheries. Thus, commercial fisheries and seals may have become important competitors of predatory fishes for the same resource.