DNA barcoding and metabarcoding have proven to be indispensable tools for characterization of diversity, both genetic and taxonomic. The relatively low cost of metabarcoding, in terms of time and money, increases its attractiveness as a tool for ecological studies. However, metabarcoding approaches are hindered by poor representation of multiple organism groups in barcode databases, particularly in fungi and lichen-forming fungi. We propose that small, regionally focused, single organism group barcode databases can help address the current lack of species representation. We assessed this for lichen-forming fungi by creating a barcode database focusing on the ITS barcoding region, made up of over 4800 sequences representing over 600 formal and provisional species. We then compared our regional database and the UNITE fungal DNA database with respect to identification success of bulk sequences from samples across the Intermountain West. The regional database successfully identified more than twice the number of the 473 recovered species hypotheses that UNITE successfully identified. We show that regional databases can be a powerful tool in filling gaps in barcode databases with broader scope, as robust regional databases can focus on single regions and single groups before being linked to wider databases.