Mitochondrial DNA (mtDNA) is a circular double-stranded genome spanning approximately 18 kb in animals and 16,569 bp in humans, encompassing 37 compact genes and 2 noncoding spacers. The gene organization exhibits almost typical gene arrangement with tRNA genes being often in clusters and protein-coding genes being interspaced with tRNA genes and noncoding spacers. The mitogenome is acquired by maternal inheritance and has a high mutation rate, high copy number, and no recombination and; therefore, it is a powerful candidate for genetic diversity of almost all animals. Besides its wide application in inferring the genetic diversity of different animal infraorders, mtDNA is a powerful tool in human forensic genetics, particularly in analysis of degraded biological samples, bone remains and identification of missing persons. Despite heteroplasmic characteristics, mtDNA SNPs can be obtained by using massively parallel sequencing technology, and therefore, it is a good tool for forensic genetics.