The whole chloroplast (cp) genome sequence of Zamia fischeri has been characterized. The cp genome length was 164,767bp in length, with a GC content of 39.7%, containing a large single copy (LSC) of 90,226bp, a small single copy (SSC) of 23,223bp, and a pair of inverted repeats (IRs) of 25,659bp. The genome contained 127 genes, including 88 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. A phylogenetic analysis based on complete chloroplast genomes in Cycads indicates that Z. fischeri clustered with another Zamia (Z. furfuracea). This complete chloroplast sequence offers a promising tool for further species identification, population genetic conservation, and evolutionary studies of Zamiaceae, as well as for Cycadales.