Every year, fungicide use to control plant disease caused by pathogenic fungi increases. The global fungicide market is now worth more than £5.3 billion, second only to the herbicide market in importance. In the UK, over 5500 tonnes of fungicide were applied to crops in 2010 (The Food and Environment Research Agency, Pesticide Usage Statistics), with 95.5% of the wheat-growing area receiving three fungicide sprays. Although dependence on fungicides to produce food securely, reliably and cheaply may be moderated in the future by further developments in crop biotechnology, modern crop protection will continue to require a diversity of solutions, including effective and safe chemical control. Therefore, investment in exploiting the increasingly available genome sequences of the most devastating fungal and oomycete phytopathogenic species should bring an array of new opportunities for chemical intervention. To date, the impact of whole genome research on the development, introduction and stewardship of fungicides has been limited, but ongoing improvements in computational analysis, molecular biology, chemical genetics, genome sequencing and transcriptomics will facilitate the development and registration of the future suite of crop protection chemicals.