The EcoTroph model leaves aside the notion of species, and models the functioning of marine ecosystems as flows of biomass from low to high trophic levels, so as to quantify easily the impacts of fishing at an ecosystem scale. In this paper, based on two case studies we present a new development of the EcoTroph model that is devoted to the analysis of fishery interactions and impacts of fleet segments on ecosystems. First, deriving an EcoTroph model from an Ecopath model of the Guinea ecosystem, the impacts of the artisanal fishery are distinguished from those of the industrial fishery. It appears that these fisheries do not always compete for the same fish groups but that they both strongly impact the ecosystem and moderately impact one another. Then, an EcoTroph model of the Southern Benguela ecosystem is set up, also based on a pre-existing Ecopath model. Two scenarios are simulated: a doubling in the fishing mortality of small pelagics and a doubling in the fishing mortality of hake. An increase in fishing mortality of small pelagics causes a strong decrease in biomass at all trophic levels of the ecosystem, confirming the pivotal role of these "wasp-waist" species in this ecosystem.