The rate of fungal infections is increasing rapidly, and pathogenesis of their species is poorly understood. Among fungi, Candida species are a major cause of morbidity and mortality worldwide and thus represent a serious threat to public health. In addition, Cryptococcus spp. are yeasts responsible for serious lung infections and meningitis. Polyenes, fluoropyrimidines, echinocandins, and azoles are used as commercial antifungal agents to treat fungal infections. However, the presence of intrinsic and developed resistance against azole antifungals has been extensively documented. The re-emergence of classical fungal diseases has occurred because of the increment of the antifungal resistance phenomenon. In this way, the development of new satisfactory therapy for fungal diseases persists as a major challenge of present-day medicine. The urgent need includes the development of alternative drugs that are more efficient and tolerant than those traditional already in use. The identification of new substances with potential antifungal effect at low concentrations or in combination is also a possibility. This chapter briefly examines the infections caused by Candida and Cryptococcus species and focuses on describing some of the promising alternative molecules and/or substances that could be used as antifungal agents, their mechanisms of action, and their use in combination with traditional drugs.