This chapter describes the study of one genetic system, mitochondrial DNA (mtDNA), within the Austronesian-speaking world, and discusses whether the patterns of genetic variation at this genetic locus are consistent with the principal models of the settlement and linguistic diversity in this vast geographical region. Mitochondria are the seat of cellular metabolism and have their own complement of DNA. MtDNA is a tiny proportion of the genetic makeup of a human being, and has both advantages and disadvantages in population studies. It is inherited maternally, in contrast with the nuclear chromosomal DNA inherited from both parents. (Note: the mitochondria of the spermatozoon are eliminated from the egg soon after fertilization, so offspring do not inherit paternal mtDNA, although there are exceptions to this rule, as shown by Schwartz and Vissing 2002.) The maternal mode of inheritance permits the study of female lineages through time.