Incidences of opportunistic fungal infections and related mortality are growing threats to immunosuppressed patients. Limited arsenal in form of antifungals, along with emerging resistance, their toxicity and efficacy are the bottlenecks in successful treatment. Thus there is an urgent need to develop new antifungal agents with no adverse effects and resistance emergence. This is possible with a better understanding of the physiology of fungi as well as mechanisms resulting in the development of multidrug resistance. Among the different mechanisms contributing to drug resistance, recently mitochondrion has been found to be crucial in determining the resistance in fungal cells. This includes mitochondrial ATP status, respiration, fission, fusion mutants, etc. The literature related to mitochondrial functioning in fungi suggests that this organelle can be targeted for future antifungal discovery.