The precise diagnosis of fungi is utmost important owing to the morbidity and mortality caused especially in various susceptible hosts. Among the diagnostic methods though the phenotypic methods are being routinely used among laboratories but they have inherent hindrances of being tedious, time-consuming and entail experience. These roadblocks acting as a major obstacle in precise identification of fungi, underlined the requisite for implementation of genotypic methods for routine diagnosis. Since sequencing forms the cornerstone of molecular identification of fungi, many sophisticated modalities and platforms have been developed. The role of fungal sequencing isn't limited merely to the identification of known fungal species in routine laboratory, but is of utmost significance in deciphering the emerging pathogenic and saprophytic fungal species that have the potential to infect humans. It was with the use of these sequencing techniques that the complex fungal nomenclature based on presence or absence of sexual form of the fungus, could be simplified and unified effort led to adoption of ‘one-fungus--one-name’ rule. Panfungal PCR targeting 28S rRNA when used in conjunction with sequencing for detection of etiological agents in patients with invasive fungal disease (IFD) from deep tissue samples has shown encouraging results. Though many sequencing modalities are available, an ideal diagnostic platform is yet awaited to meet the diversity of fungal infections in initial stages itself. The early diagnosis enables the clinician to administer appropriate therapy as and when required. The same helps in delimiting the undesired affects of antifungals as well as indirectly help in antimicrobial stewardship as well.