Taxonomic identification of spider species from morphological structures has limitations in cases of closely related species or intraspecific variability. We investigate the utility of genetic barcoding with the mitochondrial marker cytochrome c oxidase I (COI) in ghost spiders of the subfamily Amaurobioidinae. Most discrepancies between DNA barcoding and morphological identification are explained by low geographic sampling or by geographically structured lineages. In addition, we show that the marker COI is phylogenetically informative for deeper nodes in the tree. (Image credit: Martín Ramírez.)