The study of Austronesian languages classified the Sundanese language within the Malay-Sumbawa group along with Madurese, Aceh, Balinese, Sasak, Sumbawa, and Malay languages. However, The HUGO Pan-Asian SNP Consortium in 2010 reported that the genetic relationship between Sundanese and Javanese people was closer than the one between Sundanese and Malay people. The history of both kingdoms also confirmed the close relationship between Sundanese elites in the west and Javanese elites in the central and east parts of Java. Maternal lineage analysis was done on the mtDNA D-loop region (HVRI and II) from 118 unrelated Sundanese and 33 Javanese probands. We found 12 newly-formed haplotypes (or maternal lineages) as a divergence from one maternal lineage that was characterized by a normal mutation of 186C. These 12 haplotypes were commonly known as the current population of Sundanese and Javanese. Moreover, we also found 11 individual haplotypes that were predicted to be older than the common 12 haplotypes. These older haplotypes were characterized by normal mutations of C64T and C186G. Using a model of K2P, the maternal genetic distance between Sundanese and Javanese populations was 0.12555 or equal to 2190-4622 years of divergence based on the calibration of the mutation rate on both hypervariable regions.