What little we know of deep-sea ecosystems indicates that they host one of the highest biodiversities on the planet as well as important mineral and biological resources, which are increasingly being exploited. Understanding deep-sea biodiversity and ecosystem functioning, from viruses to megafauna, is essential to assess the impact of natural and anthropogenic factors and provide management options. The Mediterranean, in particular, is a unique system for such studies, characterised by homeothermia and a steep gradient of increasing oligotrophy towards the East. The aim of BIOFUN is to characterise, under an ecosystem approach, two deep-sea habitats – the mid-slope and abyssal plain – including for the first time the analysis from viruses to megafauna, to understand the linkages between biodiversity patterns and ecosystem functioning in relation to environmental conditions along a gradient of increased oligotrophy from West to East. The BIOFUN team, composed of 10 partners, proposes a multidisciplinary coordinated research programme to investigate the Algerian-Balearic Basin (1200 & 3000 m) and the Ionian Sea (1200 & 3000 m) in the Mediterranean, and the Galicia Bank in the Atlantic (1200 & 3000 m). Supplementary areas will be sampled by different partners, including the Catalan slope (NW Mediterranean), the Messina Abyssal Plain (4100 m) and the Levantine Basin. The sampling programme is based on several multidisciplinary cruises to be conducted in 2008 and 2009: two trans-Mediterranean cruises using the new Spanish RV Sarmiento de Gamboa and the Italian RV Urania, two cruises to the Galicia Bank on board the Belgian RV Belgica and the Dutch RV Pelagia and several smaller cruises in the NW Mediterranean.