Illicium anisatum L. is a neighbor species of Illicium verum used for making anti-virus vaccine. Here, we completed the chloroplast genome of I. anisatum. Its length is 142,747 bp long and has four subregions: 100,833 bp of large single copy (LSC) and 20,227 bp of small single copy (SSC) regions are separated by 10,844 bp of inverted repeat (IR) including 123 genes (81 protein-coding genes, 8 rRNAs, and 34 tRNAs). The overall GC content of this chloroplast genome is 39.2\% and those in the LSC, SSC, and IR regions are 38.1\%, 33.9\%, and 49.3\%, respectively. Twenty-one single nucleotide polymorphisms (SNPs) and 114 insertion and deletions (INDELs) are identified against I. anisatum originated from Green Farmacy Garden. Interestingly, 12 INDEL clusters, of which length ranges from 2 bp to 21 bp are identified, which is like the case of Duchesnea chrysantha. Phylogenetic trees show that five Illicium chloroplast genomes form Illicium clade, clearly.