Abstract:This paper reviews the application of high-throughput sequencing technologies in the mitochondrial genomes. Two methods using high-throughput sequencing technology are included. The first method needs to enrich mtDNA from the sample， including extraction and purification of mtDNA， PCR amplicon-based， specific-probe hybridization (microarray-based and PCR-generation probe)， then the enriched mtDNA was sequenced. For the second method， mitochondrial genome sequences were extracted from genome at first， then they were assembled using bait sequence or the mitochondrial genome sequence of related species as a reference， with software MITObim. In addition， the optimization flow chart of mitogenome sequencing using high-throughput sequencing technology was given in this paper. Finally， this paper also introduces the sequencing strategy of mixed sample.