Rubia yunnanensis Diels 1912 (Rubiaceae) is a plant used in traditional Chinese medicine. We here assembled a complete chloroplast (cp) genome for R. yunnanensis using Illumina HiSeq reads. https://www.ngetikin.com/flash-choice-1-Gallon-Roll-Cote-High-Performance-Moisture-Vapor-Barrier-Coating-and-Primer-limited-super/