Since members of the fungal kingdom play an important role in natural products research, accurate identification of these species is a critical step in revealing information about the organism under study. Based on a recent study by a multinational and multilaboratory consortium, the nuclear ribosomal internal transcribed spacer (ITS) has been selected as the DNA barcode for fungi, although recommendations for other genes where ITS might fail may be offered in the future. In this study, we sequenced the complete ITS region for species-level identification of selected fungal strains from the Mycosynthetix library that produced a range of bioactive compounds (i.e. cyclodepsipeptides, sesquiterpenoids, verticillins, tetramic acids, and resorcyclic acid lactones). These strains were previously identified using a partial region (˜300–350 bp) of the D2 divergent domain of the large-subunit nrRNA. We compared the utility of both ribosomal markers by performing a GenBank-Blastn search and Maximum Likelihood phylogenetic analysis to determine the species identities and to predict their molecular phylogenetic affinities, respectively. In addition, we examined the morphological characteristics of the fungal strains to confirm their identity. Our results suggests that ITS has a higher probability of successful identification at the species level, while D2 was slightly poorer.