The diversity of qualitative traits of Indonesian indigenous chickens was higher compared to Malaysian chickens and commercial chickens. This study didn’t able to reveal the genetic diversity of Malaysian chickens since the their sequences of mtDNA D-loop have been in progress. However, based on diversity of mtDNA D-loop sequence, the Indonesian chickens are grouped as 5 haplogroups: III (BSR, KP and PL), IV (KP, KG, GG, GK, RD, AKB), V (KB and KT), VI (KP, GK, BSR) and VII (commercial chickens). Green junglefowls (group I) and red junglefowls (group II) are predicted as common ancestors of Indonesian indigenous chickens. The establishment of Indonesian chickens need improvement in breeding and selection program appllied by breeders and farmers