Background Whole chloroplast genome or c-p-D-N-A sequence is becoming widely used in the phylogenetic studies of plant and species identification. However, in most cases the cpDNA were acquired from silica gel dried fresh leaves. So far few reports have been available to describe cpDNA acquisition from crude drugs derived from plant materials. DNA from this usually is seriously damaged during processing. The study aims to retrieve cpDNA from the commonly used crude drug Eriobotryae Folium using genome skimming technique. Methods Researchers sequenced the cpDNA from fresh leaf samples of Eriobotrya japonica and its close relatives E. deflexa, E. cavaleriei, E. fragrans. They also sequenced those of Dillenia turbinata and Magnolia grandiflora. Additionally, they sequenced the cpDNA from self-made sun-dried E. japonica leaves and three commercial crude drug polypyrrole or Pipaye or P-P-Y (PPY) samples. This was done to investigate the feasibility of cpDNA sequencing in identification of the crude drugs. Researchers also compared the efficiency of cpDNA sequencing and the general barcode. Among examples of the general barcode are the Internal transcribed spacer (ITS) and PPY identification. Key findings Researchers successfully recovered cpDNA sequences and rDNA sequences from the crude drug PPY. Bioinformatics analysis showed a high overall consistency between the cpDNA obtained from the crude drugs and fresh samples. In the maximum likelihood tree, each species formed distinct monophyletic clades based on cpDNA sequence data. Meanwhile, the phylogenetic relationships between Eriobotrya species were poorly resolved based on ITS and ITS2. Conclusion Both cpDNA and ITS/ITS2 are effective for identifying PPY and its counterfeits derived from distantly related species. However, cpDNA is more effective for distinguishing the counterfeits derived from the close relatives of Eriobotrya japonica. This supports the potential of genome skimming for retrieving cpDNA from crude drugs used in traditional Chinese medicine for identification.