Large-scale mitochondrial DNA (mtDNA) D-loop sequences data from previous studies were investigated to obtain genetic information which contributes to a better understanding of the genetic diversity and history of modern sheep. In this study, we analyzed mtDNA D-loop sequences of 963 individuals from 16 Chinese indigenous breeds that distributed seven geographic regions. Phylogenetic analysis showed that all three previously defined haplogroups A, B, and C were found in all breeds among different regions except in Southwest China mountainous region, which had only the A and B haplogroups. The weak phylogeographic structure was observed among Chinese indigenous sheep breeds distribution regions and this could be attributable to long-term strong gene flow among regions induced by the human migration, commercial trade, and extensive transport of sheep. The estimation of demographic parameters from mismatch analyses showed that haplogroups A and B had at least one demographic expansion of indigenous sheep in China.