Retrotransposons, jumping genetic elements that are amplified via RNA intermediates and randomly integrated in the genome, have been proved to be a superior strategy in resolving complicated phylogenies.Chicken repeat 1 (CR1), a member of non-LTR retrotransposon, is an important phylogenetic marker in avain systematics.The Sichuan Partridge, Arborophila rufipectus belongs to Phasianidae family, is listed as the endangered species and the first-class protected animal in china.Due to their restrict distributions of A.rufipectus in the southwest of China, very little background information has been known related to its evolutionary history and phylogenetic relationship to other Phasianidae birds.In the present study, we assembled a draft genome sequence of A.rufipectus based on pairend short sequence reads and reported for the first time the primary characteristics of repetitive elements in the species.Approximately 254,966 CR1 transposable elements were identified by the software RepeatMasker, covering 6.7% of the A.rufipectus genome.Furthermore, a comparative analysis revealed that roughly 11.50% of the Sichuan Partridge genome consisted of repetitive sequences, which were similar to that in the chicken genome and higher than in zebra finch.Additionally, a common feature of A.rufipectus, chicken and zebra finch repetitive elements is a high fraction of CRI repeats with respect to the total repeat elements.Subsequently, eighteen novel loci of CR1 elements were selected randomly by comparison of the chicken, turkey genome and the assembled A.rufipectus scaffolds to investigate their applications in Phasianidae phylogeny analysis.Here, a dataset comprising of twenty two CR1 loci, mitochondrial genomes and four unlinked nuclear segments was analyzed to infer the evolutionary relationships of twelve phasianidae species.Our results indicated that A.rufipectus is a sister clade to A.ardens/A, brunneopectus with high support values, and genus Arborophila is in a basal phylogenetic position within Phasianidae.Moreover, this study strongly supported a phylogenetic affinity between T.temminckii and T.szechenyii/L, lhuysii.However, we provided additional evidence that partridges, pheasants and tragopans were none-monophyletic lineages.Our cladograms also implied that the turkey was a member of the Phasianidae and a close relationship among C.amherstiae, S.reevesii and P.colchicus, with strong support.Therefore, this work not only resolved some of the confounding relationships in Phasianidae especially for the phylogenetic position of A.rufipectus, but also suggested that CR1 sequences can provide powerful complementary data for phylogeny reconstruction.