Over a decade of research on recent cold-water coral mounds in various oceans has set the stage for comparative studies between recent and ancient carbonate mound systems, with the aim to unravel generic processes and reveal the "red thread" in a fundamental strategy of Life building Geology a strategy nearly as ancient as Life itself. Natural laboratories have been identified in the present ocean, which provide new insights in oceanographic controls on species migration and settlement, in the interaction of currents and carbonate build-up, in the earliest diagenesis which overprints environmental signals and shapes the template of compartmentalization of carbonate build-ups, and in so many other processes and factors ultimately shaping carbonate bodies, comparable in size and properties to the large-scale carbonate hydrocarbon reservoirs in the geological record. Ocean drilling and coring is an essential component of this research. Ideally, this process is a two-way avenue between Shallow and Deep Time, where fundamental and industrial knowledge about fossil carbonate mounds can drive further investigations and even experimentation in the present seas, while the discoveries and process studies on "live" systems can yield new insights in the architecture and evolution of ancient reservoir systems. This bridging exercise is the quintessence of COCARDE (Cold-Water Carbonate Reservoir Systems in Deep Environments), an international network under the auspices of IOC-UNESCO (http://www.cocarde.eu). COCARDE has organised two workshops in 2009, with a significant support of European programmes (e.g. ESF Magellan workshop series) and partner projects (e.g. ESF EuroDIVERSITY project MiCROSYSTEMS). This special issue groups 12 papers, all addressing observations which by their nature have the potential to provide keys to generic processes, of relevance for past carbonate systems. As COCARDE proceeds, it is the objective to "reciprocate" in near future with an equivalent grouping of contributions from the study of fossil studies, to guide further research in the present ocean. It is the purpose of COCARDE to strengthen such a reflux from the studies of fossil systems by stimulating relevant continental drilling exercises, with comparable sampling protocols, resolution and analytical procedures where relevant - to allow direct comparisons with records from ocean drilling. The papers in this special issue have been structured in four themes: (i) keys to palaeoenvironmental control, (ii) mound initiation, growth and demise, (iii) of microbes and mounds, and (iv) tracking organominerals Recent and Ancient.