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[Objective] The present paper aimed to fully understand the genetic diversity and phylogenetics of Xinjiang indigenous sheep breeds, and provide theoretical basis for breeds, conservation and utilization. [Method] The squences of mitochondrial DNA (mtDNA) Cylb of 13 Xinjiang indigenous sheep breeds were amplified and sequenced. [Result] It was found that these breeds had abundant genetic diversity, except Hotan sheep. Neutral test showed that Hotan sheep had experienced population expansion. The genetic distance between Hotan sheep breeds and Qira black sheep breeds was the closest, and between Hotan sheep breeds and Bachu sheep breeds was the furthest. There were relatively far genetic distance between Bachu sheep breeds and other breeds. 13 indigenous sheep breeds were divided into 3 branches by haplotype network. After AMOVA molecular variation analysis, genetic variation between populations and within populations was 91.33% and 8.67%, respectively. There was no significant genetic differentiation among populations. [Conclusion] The results showed that there were three matrilineal origins in 13 Xinjiang indigenous sheep breeds. The genetic relationship was basically consistent with the breeding history and geographical distribution. Hotan sheep had low genetic diversity and need to strengthen the protection of germplasm resources. [ABSTRACT FROM AUTHOR]