The mechanisms governing the unprecedented 1989-90 anchovy-Mnemiopsis shift event in the Black Sea were evaluated with a coupled model of bioenergetic-based anchovy population dynamics and lower trophic food web structure. Simulations showed that a combination of direct and density-dependent effects of overfishing, eutrophication-induced nutrient enrichment, climate-induced over-enrichment and temperature-controlled Mnemiopsis spring production were involved in the shift. Eutrophication made the system vulnerable to further enrichment through the change of regional climate to a severe winter regime during 1985-87. While Mnemiopsis was acclimating to its new environment, increasing nitrate flux into the euphotic layer enhanced the carrying capacity of the system, but a disproportionate Mnemiopsis biomass increase was delayed until spring temperature conditions returned to normal in 1988-89. Enhanced carrying capacity provided a competitive advantage of food consumption to Mnemiopsis compared with anchovy, and warm spring temperature conditions promoted their spring-summer production. Prevalent high fishery pressure and increasing impact of Mnemiopsis on the food web further induced the anchovy stock collapse. However, the shift event did not result in alternation of the system to a new totally Mnemiopsis-invaded quasi-stable regime. Instead, anchovy started recovering when the subsequent strong 1991-93 cooling regime limited the Mnemiopsis population growth. Our analysis indicated that the switch of a large marine ecosystem to a totally gelatinous invader-dominated state requires extremely strong environmental perturbations. More often, environmental disturbances create a suitable niche for an alien gelatinous invader to become a member of the food web structure, and to share food resources with the native small pelagic fish community.