The genetics of marine populations is a subject that has made little progress compared with the effort spent on the terrestrial environment. This is so despite ‘‘applied’’ aspects such as stock management, marine aquaculture, creation of reserves, conservation of the coastal zones, taxonomy, and protection of species. The crowded and dispersive marine environment, with its steep physical gradients, favours the existence of a planktonic larval stage for most species. The attendant high fecundity has important consequences for selection differentials and dispersal and therefore for the evolution of genetic structures. These features must be taken into account in order to understand the origin and maintenance of marine biodiversity and, in some cases, to manage it. In this article, after a definition of genetic diversity among other aspects of biodiversity, special features of the marine environment and processes governing genetic diversity are given together with the molecular tools required to study it. Then, an overview of the interesting scientific questions in marine biodiversity research is given concerning the population structure as a function of dispersal systems and spatial constraints: gene flow and speciation in a dispersive environment, the phylogeography and historical biogeography of marine ecosystems; the functional and adaptive aspects of polymorphism: larval phase and genetic control of recruitment. Some uses of genetic diversity for assessment, conservation and protection purposes are also detailed. Organismal (specific) diversity does not enter the scope of the article.