Genetics and resilience -- Mixed stock analysis and the power of different classes of molecular markers in discriminating coastal and oceanic Atlantic cod (Gadus morhua L.) on the Lofoten spawning grounds, Northern Norway -- Contrasting levels of genetic differentiation among putative neutral microsatellite loci in Atlantic herring Clupea harengus populations and the implications for assessing stock structure -- Marine protected areas/reserves -- Marine reserves: the need for systems -- The challenge of assessing whether the OSPAR network of marine protected areas is ecologically coherent -- Individual-based movement behaviour in a simple marine reserve-Fishery system: why predictive models should be handled with care -- Effect of marine reserve protection on spiny lobster (Palinurus elephas Fabr., 1787) in a central western Mediterranean area -- Incorporating ecological functioning into the designation and management of marine protected areas -- Go with the flow: tidal import and export of larvae from semi-enclosed bays -- Seabed mapping in the southern Irish Sea: predicting benthic biological communities based on sediment characteristics -- Climate change and marine ecosystems -- Alien species in the Mediterranean Sea-which, when, where, why? -- The effect of high flow events on mussels (Mytilus edulis) in the Conwy estuary, North Wales, UK -- Mobility of metals in salt marsh sediments colonised by Spartina maritima (Tagus estuary, Portugal) -- Ecological hindcasting of biogeographic responses to climate change in the European intertidal zone -- Long-term changes in the status of Sevastopol Bay and the Crimean coast: anthropogenic and climatic influences -- Sustainable fisheries/aquaculture -- The sea ahead: challenges to marine biology from seafood sustainability -- Effects of fishing methods on deep water shark species caught as by-catch off southern Portugal -- Catch me in winter! Seasonal variation in air temperature severely enhances physiological stress and mortality of species subjected to sorting operations and discarded during annual fishing activities -- Grazing and assimilation rate estimates of hydromedusae from a temperate tidal creek system. This volume presents a representative sample of contributions to the 41st European Marine Biology Symposium held in September 2005 in Cork, Ireland. The theme of the symposium was 'Challenges to Marine Ecosystems' and this was divided into four sub themes; Genetics, Marine Protected Areas, Global Climate Change and Marine Ecosystems, Sustainable Fisheries and Agriculture. The world's marine ecosystems face multiple challenges, some natural, but many resulting from humankind's activities. Global climate change, driven by influences of energy usage and industrial practices, is a reality now accepted by most of the world's scientists, media and political establishments. Warming seas and rising sea levels are regarded as threats, while visionaries consider deep ocean carbon disposal as a technological opportunity. Exploitation of the seas continues apace, with repeated concerns over the impact of over-fishing, plus reservations about the environmental effects of marine aquaculture. We need to understand how resilient organisms and ecosystems are to these challenges, while responding by protecting biologically-meaningful areas of the oceans. The subthemes of the 41st European Marine Biology Symposium address all of these matters.