The biosphere of the ocean floor and subfloor has only been discovered in the last few decades, but is already being exploited for mineral resources. Fundamental knowledge of the biology and geology of these regions is lacking, and there is currently no coordinated approach to sample collection and analysis. A project titled 'The deep sea and sub-seafloor frontier' (DS3F) was funded by the EU to develop sampling strategies aimed at understanding the biological and geological dynamics of the deep seafloor environment. DS3F brought together scientists from fields such as marine biology and geosciences as well as administrators and funding groups to address the problem. Project work consisted of eight workshops that invited researchers to address various aspects of the marine sciences. The findings of these workshops were then brought to an overarching workshop, which condensed the findings into a white paper detailing the important tasks and directions for deep sea research. Four topics were designated as key issues in deep sea exploration and exploitation: the climate, ecosystems, geohazards and resources. The paper also identified Europe as key to this field, as it has the technology and the research potential to make a significant contribution. In order to protect biological and geological resources in the deep sea environment, substantial knowledge and a commitment to research excellence in the field is required. DS3F is the first step towards understanding, and ultimately protecting, this environment.