Identification of fungi to the species level has some challenges because of great diversity in morphology and ecology. Therefore, developing an efficient species recognition system which is applicable for all fungi seems difficult. Currently, DNA sequences of different regions have become powerful molecular data for rapid identification of specimens and overcoming the different sets of traditional criteria used for describing fungal species. However, deciding the potential region(s) as DNA barcode is a crucial step to identify biological specimens and to assign them to a given species. In the present review, usefulness of several DNA markers (ITS, LSU, SSU, COX1, RPB1, RPB2, beta-tubulin, MCM7, TEF1-alpha, gamma-actin, ATP6 and CaM genes) were investigated based on current studies. The pros and cons of each gene in Ascomycota, Basidiomycota and other fungal phyla were discussed. Even though numerous studies were completed to decide a marker as DNA barcode for a specific taxon it was observed that potential DNA barcodes vary from species to species. However, ITS was indicated by lots of studies as the potential barcode for most of fungi due to high degree of interspecific variability, conserved primer sites and multiple copy nature in the genome. Several protein-coding regions such as TEF1-alpha, RPB1, RPB2, beta-tubulin and CaM genes may be accepted as secondary barcodes for the vast majority of Ascomycota genera such as Penicillium, Aspergillus and Fusarium. Therefore, concatenated alignment of the ITS region with one or more protein-coding genes may be effective for finer-scale species-level identification of specific fungi.