The oceans play a crucial role in the global environment and the sustainability of human populations, because of their involvement in climate regulation and provision of living and non-living resources to humans. Maintenance of healthy oceans in an era of increasing human pressure requires a high-level understanding of the processes occurring in the marine environment and the impacts of anthropogenic activities. Effective protection and sustainable resource management must be based, in part, on knowledge derived from successful research. Current marine research activities are being limited by a need for high-quality researchers capable of addressing critical issues in broad multidisciplinary research activities. This is particularly true for developing countries which will require the building of capacity for marine scientific research. This paper reviews the current activities aimed at increasing marine research capacity in developing and emerging countries and analyses the challenges faced, including: appropriate alignment of the research goals and societal and policy-relevant needs; training in multidisciplinary research; increasing capacity for overall synthesis of scientific data; building the capacity of technical staff; keeping highly qualified personnel in marine scientific research roles; cross-cultural issues in training; minimising duplication in training activities; improving linkages among human capital, project resources and infrastructure. Potential solutions to these challenges are provided, along with some priorities for action aimed at improving the overall research effort.