Olive oil is the major edible vegetable oil of the Mediterranean countries that is much prized for its flavour and aroma. Olive oil, the main fatty component of the Mediterranean diet, is characterized by consisting of monounsaturated fatty acids as well as by its elevated content in antioxidant agents. The economic importance of olive oils has grown considerably in the last decade and it has become a main source of revenue for many Mediterranean countries. In this context, there is an urgent need for a better characterization of olive genetic resources and their diversity and for the implementation molecular tools for oil traceability. This database, that we named OGDD (Olive Genetic Diversity database), is a collection of data and tools on microsatellite markers that have been commonly used for assessing olive genetic diversity. These data were collected from the scientific literature and other public resources. We hope that it will be useful for a large community, including researchers, professionals and all those interested by the olive tree. We welcome all comments and questions on the database.