This theme section, ‘‘Coral reefs in a changing environment’’, stems from the ASLO Aquatic Sciences Meeting 2009 in Nice, France (January 25–30), where session # 28 (Coral reefs and coral communities in a changing environment) was chaired by Cornelia Maier, Bernhard Riegl and Christian Wild. This session included 12 oral and 9 poster contributions covering a broad range of topics, and attracted a large number of visitors. That the upcoming 2010 European ISRS meeting in Wageningen, the Netherlands, has a similar motto, ‘‘Reefs in a changing environment’’, appears to emphasize the importance and timeliness of the question: How do corals and coral reefs respond to rapid environmental change? Clearly, anthropogenically-induced climate change and pollution alter the chemistry and temperature of seawater at an unprecedented and rapid rate, and constitute a major threat to the survival of tropical, temperate and cold-water coral reefs and coral communities. CO2-induced ocean acidification and warming, along with terrestrial runoff and pollution, negatively affect health, growth and calcification of corals. However, the extent to which these indirect and direct anthropogenic stresses interact and impact corals and coral-generated reef ecosystems needs to be addressed in more detail. The following six contributions to the theme section reflect a high diversity with respect to the scientific contents on both the species and the community level. The manuscripts address the effects of the two groups of parameters linked to global climate change: firstly, indirectly anthropogenically caused effects such as surface temperature (Heyward and Negri 2010; Thompson and Dolman 2010; Naumann et al. 2010) and pH (Ries et al. 2010); and, secondly, directly anthropogenically caused effects such as inorganic nutrient concentrations (Naumann et al. 2010; Tanaka et al. 2010) or natural regular disturbances (Browne et al. 2010) on coral metabolism (Naumann et al. 2010; Tanaka et al. 2010; Ries et al. 2010), coral development (Heyward and Negri 2010) and coral reef community structure and cover (Browne et al. 2010; Thompson and Dolman 2010). In this context, the goals were to identify the relative influence of one or more of the factors related to environmental change. The articles in the theme section focusing on the factor temperature reveal that, below the bleaching threshold, it positively correlates with particulate organic matter (POM) release by scleractinian corals (Naumann et al. 2010), but may also negatively effect the development and distribution of their larvae (Heyward and Negri 2010). Thompson and Dolman (2010) highlight that temperature-induced coral bleaching events, even if they only occur in the frequency and severity of those in the recent past, may lead to a reduction of fast-growing staghorn coral cover in nearshore reefs of the Great Barrier Reef (GBR). This was supported by the finding that mass coral bleaching, in contrast to other stress events such as crown-of-thorns starfish outbreaks and cyclones, resulted in significant changes of benthic community composition and hard coral Communicated by Editor in Chief Prof. Rolf Bak