Abstract: Epimediumecalcaratum G.Y.Zhong is one of the special morphological groups of Berberaceae Epimedium. Its narrow distribution is listed as endangered species by IUCN. In this study, the chloroplast genome structure and phylogeny were analyzed in order to provide theoretical basis for its genetic protection. The results showed that the length of chloroplast genome was 164 962 bp, including large single copy（LSC） 80 562 bp, small single copy region（SSC） 17 040 bp and two reverse repeats（IRa and IRb） 33 680 bp, with a total GC content of 38.7%. A total of 139 genes were encoded in the chloroplast genome, including 94 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Three types of SSR were identified, including 68 mononucleotides, 2 dinucleotides and 4 complex nucleotides. 21 genes contained one or two introns; 94 protein-coding genes encoded 51 997 codons; Phylogenetic analysis showed that Epimedium was monophyletic, and it was closely related to the widely distributed epimedium.