The chloroplast genome of the Magnolia species from Central America has never been reported. With its local use for food flavoring, medicine, and wood, M. mexicana has been of good economic importance. In the present study, the complete chloroplast genome of M. mexicana was assembled via the genome skimming data. As a typical quadripartite structure, the plastome of M. mexicana with 159,906 bp in length includes two inverted repeats (26,554 bp) separated by a small single copy region (18,761 bp) as well as a large single copy region (88,037 bp). This chloroplast genome consists of 131 different genes, including 86 protein coding genes (CDS), eight rRNA genes, and 37 tRNA genes. The maximum likelihood phylogenetic analysis showed that M. mexicana from Central America was closely related to an evergreen species, M. odoratissima from East Asia.