Abstract: Chongqing contains five goats breed resources representing special economic and ecological characteristics. These goat breeds characteristics were researched and genetic relationships with other goats in adjacent provinces were ensured by analyzed mitochondrial DNA (mtDNA) D-loop sequences. The results indicated the goat breed resources in Chongqing have especial production performance in growth, meat quality and fecundity. The five goats breeds in Chongqing had high mtDNA diversity but the differences among breeds were significant. The near genetic distance of Youzhou dark goat and Banjiao goat indicated Youzhou dark goat may be a subline of Banjiao goat. The results of this study contribute to the knowledge of the genetic structure and correctly protecting and utilizing these goat breeds.