Amomum villosum Lour. is a medicinal herb of high economic value, which is endemic to southern China. The size of A. villosum chloroplast (cp) genome was 163,733 bp long, which consisted of long (LSC; 88,798 bp) and short (SSC; 15,353 bp) single-copy regions, separated by a pair of inverted repeats (IRs; 29,791 bp for each unit). Totally, 126 genes are annotated in the cp genome, including 88 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes (rRNAs). The overall GC content is 36.1%. The phylogenetic analysis based on 43 conserved protein-coding genes from 32 plant species recovered a consistent phylogeny on most of the nodes with previous results and indicated A. villosum as the sister species of the common ancestor of A. compactum and A. krervanh, and suggested that the cp genome data can effectively resolve the phylogenetic relationships. Our study provides a valuable resource for further study on its genetic diversification, evolution and germplasm conservation of this valued medicinal plant.