The principal limitation in forensic mitochondrial DNA (mtDNA) testing is the low power of discrimination that is obtained when common "mtDNA types" are involved in a case. Currently, an "mtDNA type" refers to the sequence within hypervariable regions I and II (HV1/HV2) of the control region, approximately 610 bp. In Caucasians, the most common HV1/HV2 type is found in approximately 7% of the population and there are 12 additional types found at greater than approximately 0.5% (ignoring HV2 C-stretch polymorphism). We are performing large scale sequencing of the entire mtDNA genome (mtGenome), approximately 16,569 bp, of individuals who have common HV1/HV2 types. Of 31 individuals with the most common HV1/HV2 type, only 3 still match after mtGenome sequencing. Similar high discrimination is seen in other common HV1/HV2 types. The sites that discriminate the various common HV1/HV2 types are generally not those that are known to vary widely in more diverse population samples. This indicates that complete mtGenome sequencing of selected HV1/HV2 types may stand as the best way for identifying maximally useful single nucleotide polymorphism sites outside of the control region. Our strategy for identifying SNP sites is useful in resolving U.S. Caucasian, Hispanic, and African American mtDNAs is discussed. We also discuss the development of homogeneous fluorogenic polymerase chain reaction assays that target phenotypically neutral sites for practical use in casework.