Until 2001, this order was thought to contain five families: Botryosphaeriaceae, Coccoidiaceae, Doditheaceae, Dothioraceae, and the Planistromellaceae.[2] Several molecular phylogenetic studies since that time have resulted in an organization restructuring of classification. In the December 31, 2007 revision of Ascomycota classification the Dothideales contains two families, the Dothidiaceae and the Dothioraceae. The Botryosphaeriaceae (order Botryosphaeriales) and the Planistromellaceae have been moved to order and family incertae sedis, respectively, pending the acquisition and analysis of additional molecular data.[3]
In 2022, Dothioraceae was classed as a synonym of Dothidiaceae. Also families (with number of genera); Neocelosporiaceae (3), Saccotheciaceae (8) and Zalariaceae (1) were added to the order.[4]