While “DNA barcodes” are often provided, the whole mitochondrial and nuclear genome are rarely considered to be included in species descriptions. This is unfortunate because whole genome sequencing of holotypes allows eternal genetic characterization of the most representative specimen for a given species. Thus, de novo genomes are invaluable added resources and important additional diagnostic characters in species descriptions, provided the integrity of the holotype specimens remains intact. Here, we used a minimally invasive method to extract DNA of the type specimen of the recently described caddisfly species Silvatares holzenthali (Trichoptera, Pisuliidae) from the Democratic Republic of the Congo. A low-cost next generation sequencing strategy was used to generate the complete mitochondrial and draft nuclear genome of the holotype. The data in its current form is an important extension to the morphological species description and valuable for phylogenomic studies.