The mitochondrial genome of Hemistasia phaeocysticola is composed of many circular chromosomes and it is suggested that ca. 500 bp of sequence region is shared among all chromosomes. In this study, the mitochondrial genome of H. phaeocysticola was amplified by the PCR with outward primers that were desinged within the ca. 500 bp shared region and those amplicons were sequenced by using PacBio.