Abstract: Investigation of the genetic diversity and systematic evolution in Chinese domestic fowls and red jungle fowls was carried out by the structure and polymorphism of mtDNA D-loop region. A 560 bp DNA fragment of control region of mtDNA from 256 individuals of 14 Chinese domestic chicken breeds and two red jungle was determined, the percentage of nucleotide A, C, G and T was 25.00％, 37.40％, 4.40％ and 33.20％, respectively. There were 44 polymorphic sites accounting for 7.86％ of total analyzed sites. Only transition and transversion but no insertion/deletion were found in this region, the ratio of transition and transversion in this study was 0.13．32 haplotypes were defined, in which 9 haplotypes were shared among some chicken populations. The diversity of haplotypes was ranged from 0 to 0964, the average diversity of haplotypes was 0.909±0.014. The average number of nucleotide divergence (K) and average nucleotide diversity (Pi) were 7.276 and 1.851％, respectively. Inter-population nucleotide divergence (Dxy) in 16 chicken populations was ranged from 0.747％ to 3.125％, whereas inter-population net nucleotide divergence (Da) in 16 chicken populations was ranged from 0.015％ to 2.633％. The results indicated that the genetic diversity of 14 Chinese domestic chicken breeds and two subspecies of red jungle fowl was very abundant and the genetic divergence was significant among populations．Analysis of genetic diversity and phylogenetic relationships among Chinese domestic fowls and red jungle fowls indicated that some Chinese domestic fowls such as Gushi chickens and Xianju chickens derived from Gallus gallus gallus, other Chinese domestic fowls such as Chahua chickens and Tibetan chickens derived from Gallus gallus spadiceus. The genetic contribution of these two subspecies of red jungle fowl can be detected in some Chinese chicken populations. The results indicated that the Chinese domestic fowls don′t just derive from red jungle fowl in Thailand or just from red jungle fowl in China.