Chicken genetic resources are gradually decreasing in genetic diversity; thus, a theoretical basis for conservation is needed. The genetic diversity and phylogeography of domestic chickens from 10 countries in Asia and red jungle fowl were investigated by analyzing the mitochondrial DNA D-loop hypervariable segment (HVS). The order of domestic chickens distributed in 31 management units in Asia in terms of conservation priority was assessed based on genetic diversity and genetic contribution rate models. A total of 219 haplotypes were distributed in seven clades, with variants identified at 103 sites. Phylogenetic analysis revealed seven maternal origins of Asian domestic chickens. Multiple subspecies of red jungle fowl were involved in the domestication of chickens in the three centers of origin: the Indian subcontinent (clade D), China (clades B, C, E and F) and Southeast Asia (clade A). The domestication center of the G clade remains unknown. The order in terms of conservation priority based on genetic diversity was as follows: northwestern and northeastern Yunnan, China; Sri Lanka; Guangxi, China; Japan; etc. The order in terms of conservation priority based on the genetic contribution rate was as follows: northwestern Yunnan, China; Sri Lanka; Japan; Papua New Guinea; etc. This study provided new insights for the conservation and evaluation of native genetic resources.