Magnolia fordiana var. hainanensis (Dandy) Noot. (Magnoliaceae) is an endemic and ornamental tree distributed in Hainan, China. In this study, we report and characterize the complete plastid genome sequence of M. fordiana var. hainanensis in order to provide genomic resources helpful for promoting its conservation and garden utilization. The complete plastome is 160,157 bp in length and contains the typical quadripartite structure of angiosperm, including two Inverted Repeat (IRs) regions of 26,573 bp, a Large Single-Copy (LSC) region of 88,255 bp and a Small Single-Copy (SSC) region of 18,756 bp. The plastome contains 114 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene and 4 unique rRNA genes. The overall A/T content in the plastome of M. fordiana var. hainanensis is 60.70%. The complete plastome sequence of M. fordiana var. hainanensis will provide a useful resource for the conservation and garden utilization of this species as well as for the phylogenetic studies of Magnoliaceae. [ABSTRACT FROM AUTHOR]