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 worlds marine ecosystems face multiple challenges, some natural, but many resulting from humankinds activities. Global climate change, driven by influences of energy usage and industrial practices, is a reality now accepted by most of the worlds 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.