D-loop region of mitochondrial DNA (mtDNA) consists of hypervariable segment I (HVSI) and HVSII, has been widely influenced the development of bioetnoantropologi science, genetics, molecular biology, and forensic medicine. Previous studies have determined the nucleotide sequence in HSVI and HVS2 D-loop to various ethnic groups in Indonesia, except for Papua. In this study the nucleotide sequence shown Dloop: HVS1 and HVSII in some ethnic in Papua. This research was conducted in four phases namely isolation and preparation of the individual Papuan mtDNA template, amplification of mtDNA template in vitro by PCR using M1 and HV2R primers, sequenced by Sanger method Dideoxy method using Automatic DNA Sequencer, and nucleotide sequence analysis of mtDNA using DNASTAR software. Results mtDNA sequence analysis of human mtDNA samples of ethnic Papuans produce 820-858 nucleotides of D-loop. Normal specific mutations, among others: the sample Papua namely C16. 223t, C16. 295t, T16. 362c, T16. 519c, A73G, T146c, T199c, and A263G. These mutations can be used as an indicator to distinguish human-specific mutation with a variety of ethnic Papuans in Indonesia and the World Populations. Outcomes obtained from this research is a sequence of mtDNA and polymorphism individuals on ethnic Papuans and databases that can be used directly for the benefit of the field of forensic medicine, police, population, and other related fields.