The complete chloroplast genome sequence of Yunnanopilia longistaminea, an endemic species in southwest China, is presented in this study. The total genome size of Y. longistaminea was 148,503 bp in length, with a typical quadripartite structure including a pair of inverted repeat (IRs, 28,075 bp) regions separated by a large single copy (LSC, 84,547bp) region and a small single copy (SSC, 7805 bp) region. The all GC content was 37.3%. The genome contains 117 genes, including 72 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, 13 genes contain a single intron, and 3 genes have two introns. Further, a maximum-likelihood (ML) phylogenetic tree results that Y. longistaminea was closely related to the genera of Champereia manillana.