With Amomum villosum (genus Amomum, family Zingiberaceae) as material, we obtained the complete chloroplast genome sequence using Illumina Hiseq 4000 sequencing platform, and then assembled, annotated, and characterized by bioinformatic methods. This study clarified the genetic relationship among species of Zingiberaceae, and provided scientific basis for the study of phylogeny and species identification of genus Amomum. The results showed that: (1) the total length of chloroplast genome was 164 069 bp and the GC content was 36.1%, including a pair of 29 959 bp reverse repeat region (IR), a large single copy region (LSC; 88 798 bp) and a small single copy region (SSC; 15 353 bp). A total of 133 genes were annotated, including 8 rRNA genes, 38 tRNA genes and 87 protein coding genes. (2) 157 SSR loci were detected in the A. villosum genome, and most of the SSR was composed of A and T. The cp genome size and IR boundary of genus Amomum were highly conserved, while nucleotide variability mainly occurred in LSC and SSC regions. (3) The maximum likelihood method (ML) cluster analysis showed that A. villosum had the closest genetic relationship with A. compactum and A. krervanh, and had a close relationship with genus Alpinia.