Studies and comparative analysis of DNA mutations t hat occur in the human mitochondrial genome in huma ns of Indonesia, the ethnic Papua and its comparison with several ethnic world has done. The purpose of this study to analyzed variants of the mutation in some areas on intragenic and coding region between genes in human mitochondrial genes and gene control regions using mitochondrial genome amplification techniques. Here , we reported the results of sequencing the human nucleo tide Papua, which was then compared against several individuals representing several ethnic groups in t he world. DNA samples isolated from several human t issues and then sequenced using an efficient two pairs of prim ers to amplify the mtG humans. mtG sequences are al igned and compared with rCRS using DNAstar program. Results o f analysis reveals the fact that there are mutation s outside the region HVS1 and HVS2 D-loop mtDNA ie in regions between genes. Regions between genes is the gene c oding region of the human mtG and exhibit a high mutation rate against rCRS. This opens up a new paradigm fo r the analysis of mutations in regions intragene, interge ne, and the coding regions of genes other than the D-loop mtG. Segment intragene gene located on the shorted area can be selected for studies in population genetics, forensic medicine and bioetnoantropology studies, in additio n to the area HVS1/ HVS2 D-loop that has been used. Studies in humans have to complete the data Papua mutation and polymorphism data GenBank/NCBI and other nucleotid e sequence data providers such as EMBL and DDBJ.