In recent, large case series of fungal endophthalmitis (FE) that were published by Asian authors, the most frequent etiologic agents for all types of FE are molds (usually Aspergillus species, while Fusarium is the prevalent etiology in keratitis-related FE). Candida was the organism found in most cases of endogenous FE. However, we must keep in mind that prevalence of fungal species varies with the geographical area. Lately, polymerase chain reaction (PCR) was increasingly used for the diagnosis of FE, allowing for very high diagnostic sensitivity, while the costs become more affordable with time. The most important shortcoming of PCR—the limited number of pathogens that can be simultaneously searched for—may be overcome by newer techniques, such as next-generation sequencing. There are even hopes of searching for genetic sequences that codify resistance to antifungals. We must not forget the potential of simpler tests (such as galactomannan and β-d-glucan) in orienting towards a diagnosis of FE. There are few reports about the use of newer antifungals in FE. Echinocandins have low penetration in the vitreous cavity, and may be of use in cases of fungal chorioretinitis (without vitritis), or injected intravitreally as an off-label, salvage therapy.