Statistical support is generally higher when based on a dataset of entire mitochondrial genomes than on the original barcode region or even extended barcode. With declining costs of Next-Generation Sequencing (NGS), increasing numbers of individuals will be sequenced on a massive, global scale and the mitochondrial genomes will often be the first to be assembled due to their small size. For species identification, we propose that the popular 658 bp barcode be replaced by a “Next-Generation barcode”; i.e. shallow whole genome sequencing, resulting in the assembly of the entire mitochondrial sequence and other nuclear genes as well as species delimitation by alignment-free methods.