The characterization of the mode-of-action of antifungal drug candidates - also termed target deconvolution - is an integral part in the pharmaceutical drug discovery pipeline. The classical methods that were used during decades for deciphering antifungal drug mode-of-action relied specifically on classical microscopy, basic biochemical and biophysical approaches and classical forward genetics. With the era of functional genomics and high-throughput experimentation technologies, the implementation of large-scale target deconvolution strategies has drastically reshaped the field of drug discovery. In particular, the individual or combined use of chemogenomics, high-throughput drug-target interaction assays, transcriptomics and high-throughput imaging, together with powerful computer-based approaches for the integrative and predictive analyses from multiple data, offer a completely new vision on the potential and perspectives of exploring drug-target interactions in drug discovery and chemical biology. In this chapter, an overview of the classical approaches in antifungal drug mode-of-action studies is presented as a historical perspective, followed by description of the modern, currently used or likely to be more developed, approaches for conducting large-scale antifungal drug candidate target deconvolution studies.