Pathogenic Candida species remain a significant medical problem despite the availability of antifungal therapies. Two key issues must be addressed to improve the treatment of life-threatening systemic Candida infections. First, advanced diagnostic tools are required to facilitate the early identification of these infections, when therapeutic intervention is more likely to be effective. Second, improved antifungal therapies are needed. These therapies, which might include combinations of antifungals, need to be less toxic to the patient and more potent in killing a broader range of Candida species. Recent advances in unravelling the genomics of these species should facilitate efforts to achieve these goals. We discuss the contribution of genomics to the development of novel antifungals and new diagnostic tools.