Culture independent diagnostic tests (CIDTs) for fungi include assays that detect fungal cell wall components, organism-specific nucleic acid or the host antibody response directly. This chapter comprehensively reviews the test performance of current CIDTs targeting Candida and Aspergillus species. Additionally, we examine the evidence in support of biomarker-driven preemptive antifungal therapy as well as discuss the advantages and practical limitations of available CIDTs.