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Physalis philadelphica Lam. has horticultural importance because of its edible fruits. Cultivated and wild populations grow in Mexico. In this study, the complete plastome nucleotide sequence of wild plants was generated using the IonTorrent PGM sequencing technology. The plastome size was 156,804 bp and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat regions (25,595 bp) separated by a large single copy region (87,131 bp) and a small single copy region (18,483 bp). The chloroplast genome included 80 protein–coding genes, four rRNAs, and 31 tRNAs. The phylogenetic analysis based on 19 Solanaceae chloroplast genomes recovered a clade with all Physalis species. This work revealed the importance of the plastome sequence to solve infrageneric phylogenetic relationships.