Diversity and association genetics studies lead to manipulate a large number of individual, lines, clones and/or populations. Moreover, emergence of high-throughput technologies for both genotyping and phenotyping generates a large amount of data. These need to be stored and managed in order to perform requests and organize datasets to conduct association genetics studies. The Thaliadb database has been developed with this aim. It manages genetic resources, phenotyping and genotyping data, and also population structure information. Thaliadb enables data extraction in formats used by genetic association software.