The utility of mtDNA in forensic identifications is limited by its low power of discrimination and the absence of high quality mtDNA databases. Single nucleotide polymorphisms (SNPs) in the control region outside of hypervariable regions I and II (HVI/HVII), and in the coding region of the mtDNA genome, can provide additional discrimination in mtDNA testing. We have identified particularly useful SNP sites via high throughput sequencing of the entire mtDNA genome. We report here two cases in which an 11-plex SNP assay (panel "A") targeting the most common HVI/HVII type successfully resolved two cases in which identifications could not be made on the basis of HVI/HVII sequencing. Additionally, we established a database of 286 samples for SNP panel "A" generated with robotic protocols. We have addressed the need for high quality mtDNA control region (CR) databases by developing robotic protocols for lab processing, and a carefully devised electronic data review process. A large-scale databasing effort targeting several populations underrepresented in current mtDNA databases is underway.