Due to their ease of sequencing and high levels of nucleotide diversity mitochondrial (mt) genes have long been favoured targets for investigations of species level issues in systematic entomology particularly species delimitation and diagnostic identification. Advances in sequencing technology and price reductions have now made routine sequencing of whole insect mt genomes feasible and thus the application of much larger datasets to these perennial problems can be attempted. I will present two examples – the development of diagnostic targets within forensically important blowflies (Diptera: Calliphoridae) from scans of whole mt genome variability and the determination of species status within the cotton bollworm (Lepidoptera: Noctuiidae: Helicoverpa) – to illustrate the ease and comparative cheapness of genomics level approaches to these age old problems.