Evidence is mounting that changes in the structure of marine food webs at all trophic levels have the potential not only to influence the dynamics of key trophic players but as well impact upon the transport and sequestering of carbon via changes in flux dynamics. These food webs can be affected to varying degrees by factors such as short-term environmental variability, long-term climate change, and changes in predator prey interactions, introduced species, fishing and pollution. At present, it is difficult to understand direct and indirect controls on food webs across all scales. It is also not clear whether it will be possible to understand the full ramifications and feedbacks caused by natural and anthropogenic perturbations of the marine environment. Among others, important current and future research issues on marine end-to-end food webs are (i) why we need to tackle end-to-end food webs in our studies at this time, (ii) what the key challenges are and how we can meet them, and (iii) how we can make headway in the experimental, observational and modelling components of marine end-to-end food webs.