The evolution of ecosystems are often driven by key components or species. Because of their interaction with numerous elements of the food web and their high productivity, cephalopods may be a structuring component in marine ecosystems, as they have a key role in the transfer of nutrients through trophic levels. While catches of many stocks have declined or plateaued, the captures of cephalopods have strongly increased since the 70s. However, they are prey or predators of many other fisheries resources. Building a clear understanding of their role in ecosystems is thus a key challenge for the future of Ecosystem-Based tools for fisheries and marine resource management. We highlight the important lack of understanding of the impact of cephalopods on food webs around the world and the poor implementation of the cephalopod taxa in ecosystem models. The ecology of cephalopod, and thus their role in food webs, strongly depends on their habitat. The inclusion of cephalopod groups from different habitats in an ecosystem model of South Eastern Australia confirms this idea. On one hand, some oceanic squid species have a key role in the transfer of nutrients up trophic levels, acting as a link between neritic habitats and open waters, and between pelagic and benthic habitats. On the other hand, neritic species are more locally constrained and have a variable role in nutrient transfer. While most ecosystem models are built with one single group for ‘cephalopods’ or ‘squids’, these results prove that there is a need for investing in greater details the different cephalopod ecological groups to properly assess the various roles of key species with different habitats and ecology. This is a key point of improvement for ecosystem models and management tools as cephalopods are likely to adapt relatively fast to changing conditions, including climate change and fishing pressure.