Molecular species identification is a powerful tool in taxonomy, biodiversity research and ecology, in particular for groups of organisms with limited diagnostic features. This tool relies on the development of high-quality reference sequence databases, and such databases can be built using collection specimens and mass parallel sequencing. Here, lichen herbarium specimens and mass parallel sequencing were used to generate reference ITS sequences for microlichens from the Australian Capital Territory (ACT) and to develop a reference sequence database. The preliminary database was then tested on un-identified specimens collected during the 2018 ACT BushBlitz expedition. Challenges met during both database development and molecular species identification suggest that these processes will not be straightforward for microlichens, due to the high number of sequences generated for non-target species (lichen-associated fungi, co-occurring lichenised species and sample cross-contaminants). Keywords: Australia, ITS barcode, PacBio amplicon sequencing, collection specimens.